from:"SHAHIN NASR"

[Freesurfer] citation for mris_pmake

2015-08-01 Thread SHAHIN NASR

Dear Surfer,
I want to cite the methods used in mris_pmake command but I can't find
it in wikisurfer or the help of this command.  Is the method used in this
command described in a published paper?

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] isxconcat-sess

2015-07-06 Thread SHAHIN NASR

Hi Surfers and Doug,
I was trying to average two scan sessions of the same subject and
isxconcat-sess under dev-env failed again.  This time I get this message:

ERROR: cannot find
/autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.lh/nmask.dat

Which is true! this file does not exist.

Regards



On Thu, May 14, 2015 at 10:39 PM, SHAHIN NASR sha...@nmr.mgh.harvard.edu
wrote:

 Hi Doug,
 It works without any error.

 Thanks a lot

 On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu wrote:

 I just made a fix. Can you try it out and let me know if it works?

 On 05/14/2015 11:38 AM, SHAHIN NASR wrote:
  Hi,
 Does anyone know what has changed in isxconcat-sess command in
  nmr-dev-env? Previously I could use it to average different sessions
  of the same subject. But now I am getting this error:
 
  INFO: trgsubject is self, this will fail unless all sessions are the
  same subject
  ERROR: cannot find
 
 /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz
 
  Regards
  --
  Shahin Nasr
 
  PhD in Cognitive Neuroscience
  Martinos Imaging Center, MGH
  Harvard Medical School
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School




-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] Freesurfer next version

2015-06-21 Thread SHAHIN NASR

Hi Freesurfer developers,

As far as I see, pRF (population receptive field) mapping is not a part
of current freesurfer (please correct me if I am wrong).  I was wondering
if you have any plan to add it to the next/upcoming freesurfer version?

Regards
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] mris_pmake Error

2015-05-20 Thread SHAHIN NASR

Hi Surfers,
I am using mris_pmake (in nmr-dev-env) to measure the distance between
two vertices.  Everything is fine as long as I use just one terminal.  But,
to accelerate my analysis, I have divided my analysis into multiple parts
and run each part in one terminal.  It means, I may run multiple (tens of)
mris_pmake simultaneously (in different terminal or in separate jobs in
launchpad).  This results this error:

*System error: Address already in use*

*Fatal error encountered.*
* SSocket `Unnamed SSocket_UDP_receive' (id: 0)*
* Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive*
* Problem binding to socket 1701*
*Error returned from system: Address already in use*
*Socket object name: Unnamed SSocket_UDP_receive*
*Socket object id: 0*
*Socket object type: c_SSocket_UDP_receive*
*Socket protocol: Datagram*
*Socket ID: 8*
*Throwing exception to (this) with code 1*

*terminate called after throwing an instance of 'c_SSocket*'*
*Abort (core dumped)*

How can I avoid this error?  I know I can re-do the analysis (when I see
this error) and repeat it till I get an answer.  But it slows down
everything.  So, I just want to know how I can avoid it!

Regards

P.S.: The command that I use it like this:
mris_pmake --subject Sbj --hemi lh --surface smoothwm --mpmProg pathFind
--mpmArgs vertexStart:Vert1,vertexEnd:Vert2 --mpmOverlay euclidean

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] isxconcat-sess

2015-05-14 Thread SHAHIN NASR

Hi,
   Does anyone know what has changed in isxconcat-sess command in
nmr-dev-env?  Previously I could use it to average different sessions of
the same subject. But now I am getting this error:

INFO: trgsubject is self, this will fail unless all sessions are the same
subject
ERROR: cannot find
/cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz

Regards
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] isxconcat-sess

2015-05-14 Thread SHAHIN NASR

Hi Doug,
It works without any error.

Thanks a lot

On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:

 I just made a fix. Can you try it out and let me know if it works?

 On 05/14/2015 11:38 AM, SHAHIN NASR wrote:
  Hi,
 Does anyone know what has changed in isxconcat-sess command in
  nmr-dev-env? Previously I could use it to average different sessions
  of the same subject. But now I am getting this error:
 
  INFO: trgsubject is self, this will fail unless all sessions are the
  same subject
  ERROR: cannot find
 
 /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz
 
  Regards
  --
  Shahin Nasr
 
  PhD in Cognitive Neuroscience
  Martinos Imaging Center, MGH
  Harvard Medical School
 
 
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  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] binary noise regressor

2015-05-06 Thread SHAHIN NASR

Hi Doug,
Sorry to interrupt you again with this topic.  Don't you think, to
regress out my unwanted event (eletric shock), I need to convolv this event
with the hrf model and then use the outcome as my regressor?

Regards

On Fri, May 1, 2015 at 12:23 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:

 I don't necessarily think the exclude file is a better approach. What you
 are doing is probably fine.
 doug

 On 5/1/15 12:12 PM, sha...@nmr.mgh.harvard.edu wrote:

 Hi Doug,
 The reason that we did not use that 'exclusion method' was that, we
 were not sure if the effect of shock is limited to that specific TR.
 Actually, like other stimuli/events, we expected shock effect to appear
 slightly (1-2 TRs) later.  In this case, don't you think using a
 regressor is a safer approach?
  To clarify, I am very open to your suggestions if you have a better
 idea or if you still think that exclusion is a better approach.




  That will do what you want if you expect the shock to have the same
 response to each application. Alternatively, you can set up a time point
 exclude file to exclude those time points. If you use this, then create
 the file by putting the time in seconds of the time points you want to
 exclude.
 doug

 On 5/1/15 11:45 AM, SHAHIN NASR wrote:

 Hi Surfers
  I want to remove the possible effects of a binary noise (electric
 shock) from the evoked fMRI.  To do so, I have generated a regressor
 file in which all TRs in which electric shock has been applied are
 marked as 1 and the rest of TRs are 0.  I just want to be sure that,
 this is all I need to do for the regressor!
 A sample regressor file is attached.  It has 98 rows corresponding
 to 98 TRs that we have in the experiment!

 Regards

 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School









-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] binary noise regressor

2015-05-01 Thread SHAHIN NASR

Hi Surfers
I want to remove the possible effects of a binary noise (electric
shock) from the evoked fMRI.  To do so, I have generated a regressor file
in which all TRs in which electric shock has been applied are marked as 1
and the rest of TRs are 0.  I just want to be sure that, this is all I need
to do for the regressor!
   A sample regressor file is attached.  It has 98 rows corresponding to 98
TRs that we have in the experiment!

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School


ShockNUI_Fin
Description: Binary data
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[Freesurfer] Measuring the distance relative to a path

2015-04-21 Thread SHAHIN NASR

Hi Surfers,
I need to measure the ''minimum' distance between a cortical vertex and
a manually defined path (e.g. V2-V3 border).  Is there any command or
straightforward way to do that?

Thanks
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] -per-run analysis in native space

2015-04-01 Thread SHAHIN NASR

Hi Doug,
Selxavg3-sess started without any problem but then I faced the below
error.  Do you know what is the problem?

Global In-Mask Mean = 1316.7 (8.68411)
Rescale Target = 100
RescaleFactor = 0.0759477
OLS Residual Pass
  run 1t= 0.0
Saving rho1
  run 2t=144.1
Saving rho1
  run 3t=289.9
Saving rho1
  run 4t=432.6
Saving rho1
  run 5t=580.0
Saving rho1
  run 6t=731.8
Saving rho1
  run 7t=884.9
Saving rho1
  run 8t=1042.3
Saving rho1
  run 9t=1194.9
Saving rho1
  run 10t=1341.4
Saving rho1

Smoothing ACF
/usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz
--i
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz
--o
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz
--fwhm 20.00 --smooth-only
/usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz
--i
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz
--o
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz
--fwhm 20.00 --smooth-only: Segmentation fault
voxelvolume 1 mm3
Loading mask
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz
Search region is 708874 voxels = 708874.00 mm3
Smoothing input by fwhm=20.00, gstd=8.493218
Segmentation fault (core dumped)

ERROR: /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz
--i
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz
--o
/autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz
--fwhm 20.00 --smooth-only
 --
ERROR: fast_selxavg3() failed\n



On Fri, Mar 27, 2015 at 3:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 Yes. Note that that will produce huge files (float images 256^3 by number
 of time points).
 doug


 On 03/27/2015 01:50 PM, SHAHIN NASR wrote:

 Hi Surfers,
 I want to find a way to analyze subcortical activities in native
 space and still take advantage of per-run registration.  As far as I
 understand, this is not possible in current preproc-sess.  We need one
 extra step in which we have to map all fmcpr.nii.gz files to subject's
 orig.mgz.  I am trying:

 mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz --fstarg orig.mgz
 --reg register.dof6.dat --no-save-reg --interp trilin

 in my mind, it is equivalent of what preproc-sess does when we use
 -mni305 flag (it uses mri_vol2vol to map fmcpr to mni space).

 Am I right?

 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] registration problem

2014-11-14 Thread SHAHIN NASR

Hi,
For one of my subjects, I have noticed a misalignment between sig.nii
and orig.mgz when I try to show the sig map using either tkmedit (as below):

cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis
tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45

 or tkmedit-sess:

cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects
tkmedit auil_anat orig.mgz -overlay
auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg
auil2/bold/register.dof6.dat~

I checked the registration file for this subjects and I don't see this
problem there.

tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov
../Subjects/auil2/bold/template.nii.gz --surf

I also checked the brain.mask and it covers the whole brain and looks fine
to me. I also checked my other subjects and their results are fine.

Do you have any idea why this is happening?

P.S.: I process my data in in nmr-dev-env but I have also checked the above
lines in nmr-stable53-env and problem is still there.

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] FIR analysis on regions of interest...

2014-10-14 Thread SHAHIN NASR

Hi Joe,
   I assume that you have already 1) defined your FIR function
(mkanalysis-sess) and applied it (selxavg3-sess).  I also assume that you
have already defined your ROIs (funcroi-config) and applied them
(funcroi-sess).  Up to this point, everything is more or less easy. Now,
you want to know how to get your time course!
   You have to use funcroi-table-sess command multiple times!  For FIR
analysis, you have to add '-frame X' to your funcroi-table-sess command
with X referring to the point in your time course (use funcroi-table-sess
--help for more help).  You have to repeat this command for each TR in your
time course. For example if you have 10 TR, then you have to repeat it 10
times with '-frame 0' to '-frame 9'.  Please note that, you have to save
the results in 10 different files and then read them later somehow (I use
matlab for that) and combine them to make your time course.

Let me know if you faced a problem
Good Luck



On Tue, Oct 14, 2014 at 10:24 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:


 It is still possible but not quite as easy. You have to create a
 contrast for each tap in the FIR, then run funcroi for each tap.
 doug


 On 10/14/14 7:02 PM, Joseph Andreano wrote:
  Hi All,
 
  I'm trying to extract signal from an ROI in an analysis that I specified
  as FIR.  Using funcroi-config and funcroi-table-sess, I'm able to produce
  an output file that gives me a single value for each participant.  What
  I'm trying to do is to get a value for each TR in the time window I
  specified so that I can generate a time course for that ROI.  I know that
  this was possible with the older analysis tools in the older version of
  freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are
  just giving me a single (presumably averaged) value.  Does anyone know
 how
  I can get a timecourse for my ROI?
 
  Thanks,
  Joe
 
 
  _
 
  Joseph M. Andreano, PhD
  Postdoctoral Researcher
  Interdisciplinary Affective
  Science Laboratory
  Massachusetts General Hospital
  _
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-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread SHAHIN NASR

Hi Doug,
Sorry for interrupting you again with this topic but recently we
changed couple of parameters in our MRA to increase our chance or detecting
veins. The problem is that, bbregister can not register the MRA volume to
T1 scans anymore.

As an example, here you can see the old version of our MRA and how good
it was when we used T1+pial registeration:

tkregister2 --mov
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii
--reg
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/register_t1_pial.dat
--surf

And here, you can see the new one:

tkregister2 --mov
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/001_nu.nii
--reg
/cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/register_t1_pial.dat
--surf

Now I have two questions:
1) Is there anyway to improve this registration?
2) Since I collect both MRA types in one session, can I use the good volume
(or registrations) to help registering the second volume? I actually used
--init-reg but it did not help.

Regards

On Wed, Aug 20, 2014 at 5:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:

Using --t2 and --bold will always give identical results. If there is not
much G/W contrast in the MRA (and there probably isn't), then you can try
using the pial surface instead (maybe more GM/CSF contrast). Use --surf
pial --t1. Use --t1 here because the GM will probably be brighter than CSF.

doug

On 08/20/2014 04:54 PM, SHAHIN NASR wrote:

Hi Surfers
I want to use bbregister to register my MRA scans to the structural
scans. The first attempts by using these parameters came out OK but not
perfect:

bbregister --s Subject_ID --mov MRA.nii --init-fsl --reg register.dat
--bold

However, there are obvious problems around frontal areas.

I have to admit that one of the reasons for this imperfect registration
may be that MRA scans do not cover the whole brain. However, they still
cover a large portion of it. I was wondering if there is any argument in
bbregister command that may help me improve the quality. It is very fine
if it increases the registration time.

Regards

P.S.: using --t2 in bbregister (instead of --bold) generated the same
outcome but --t1 was completely off.
--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread SHAHIN NASR

For the record, I applied two changes:

1) I used my AAScout scan as --int and it worked.
2) As you suggested I also used --t2 rather than --t1 this time and it also
helped.

Combination of these two changes worked very well.

Thanks

On Tue, Sep 30, 2014 at 1:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:


 A couple of suggestions ...

 It looks like the new sequence is T2 weighted, so you can try using --t2
 with the white surface

 It may be that the fsl is not initializing the BBR registration properly.
 Try using spm (which may still fail because it is partial brain coverage).
 Do you have a whole-brain volume that was acquired during the same session
 as the MRA? If not, you should start collecting this. If so, then use that
 as an intermediate (--int). It will use fsl/spm to register the whole-brain
 to the anatomical using standard volume reg, then transfer that
 registration to the partial FoV assuming that the whole and partial share a
 scanner space (which they will if acquired at the same time). The
 intermediate can be anything, eg, fMRI, anatomical, B0 map, low-b DTI
 volume.

 doug






 On 09/30/2014 12:41 PM, SHAHIN NASR wrote:

 Hi Doug,
 Sorry for interrupting you again with this topic but recently we
 changed couple of parameters in our MRA to increase our chance or detecting
 veins.  The problem is that, bbregister can not register the MRA volume to
 T1 scans anymore.

 As an example, here you can see the old version of our MRA and how
 good it was when we used T1+pial registeration:

 tkregister2 --mov /cluster/tootell/pitcairn/1/
 shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii
 --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/
 auil_2/MRA_500_pre_contrast/010/register_t1_pial.dat --surf

 And here, you can see the new one:

 tkregister2 --mov /cluster/tootell/pitcairn/1/
 shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/001_nu.nii
 --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/
 auil_2/MRA_TOF_2D_500_fa70_cor/018/register_t1_pial.dat --surf

 Now I have two questions:
 1) Is there anyway to improve this registration?
 2) Since I collect both MRA types in one session, can I use the good
 volume (or registrations) to help registering the second volume?  I
 actually used --init-reg but it did not help.

 Regards

 On Wed, Aug 20, 2014 at 5:06 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 Using --t2 and --bold will always give identical results. If there
 is not much G/W contrast in the MRA (and there probably isn't),
 then you can try using the pial surface instead (maybe more GM/CSF
 contrast). Use --surf pial --t1. Use --t1 here because the GM will
 probably be brighter than CSF.

 doug



 On 08/20/2014 04:54 PM, SHAHIN NASR wrote:

 Hi Surfers
  I want to use bbregister to register my MRA scans to the
 structural scans.  The first attempts by using these
 parameters came out OK but not perfect:

 bbregister --s Subject_ID --mov MRA.nii --init-fsl --reg
 register.dat --bold

 However,  there are obvious problems around frontal areas.

 I have to admit that one of the reasons for this imperfect
 registration may be that MRA scans do not cover the whole
 brain.  However, they still cover a large portion of it. I was
 wondering if there is any argument in bbregister command that
 may help me improve the quality.  It is very fine if it
 increases the registration time.

 Regards

 P.S.:  using --t2 in bbregister (instead of --bold) generated
 the same outcome but --t1 was completely off.
 -- Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School


 -- Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





-- 
Shahin Nasr

Re: [Freesurfer] fieldsign map display

2014-09-04 Thread SHAHIN NASR

Hi,
Have you ran fieldsign-sess after your selxavg3-sess?


On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini 
francescastrapp...@gmail.com wrote:

 Dear all,

 I'm trying to display the fieldsign map. I used standard
 rotating-wedge and expanding-ring paradigm, and I followed the steps
 described in FsFastIndividualRetinotopy Analysis.
 I'm running freesurfer on Ubuntu 14.04.

 Polar angle and eccentricity map look good but I can't properly
 display the fieldsign map as an alternation of two colours. I attached
 a screen-shot as example.

 Any suggestion?

 Thanks for the help!
 Francesca

 The command line is;
  tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign

 and that's the output:

 shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy
 tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign
 Surface DM lh
 Map Surface DM lh
 $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $
 Linux shalim-ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15
 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
 Tue Sep  2 17:28:57 IDT 2014
 /usr/local/freesurfer/bin/tksurfer

 list fieldsign
 con/map fieldsign

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
 maplist
 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
 mri_concat
 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz
 --o
 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
 ninputs = 1
 Checking inputs
 nframestot = 1
 Allocing output
 Done allocing
 nframes = 1
 Writing to
 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
  cd /usr/local/freesurfer/fsfast/MeytalRetinotopy
 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
 tksurfer DM lh inflated -overlay

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
 -label-outline -colscalebarflag 1 -annot aparc -fthresh 0.5 -fmid
 2.2500 -fslope .28571428571428571428 -mask

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz
 -mask-thresh 0.5 -fthresh .01

 Contrasts
 0 fieldsign


 setting colscalebarflag to 1
 setting fthresh to 0.5000
 setting fmid to 2.2500
 setting fslope to 0.2857
 mrismaskfile
 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz...
 setting mrismaskthresh to 0.5000
 setting fthresh to 0.0100
 subject is DM
 hemiis lh
 surface is inflated
 surfer: current subjects dir: /usr/local/freesurfer/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /usr/local/freesurfer/fsfast/MeytalRetinotopy
 checking for nofix files in 'inflated'
 Reading image info (/usr/local/freesurfer/subjects/DM)
 Reading /usr/local/freesurfer/subjects/DM/mri/orig.mgz
 surfer: Reading header info from
 /usr/local/freesurfer/subjects/DM/mri/orig.mgz
 surfer: vertices=118099, faces=236194
 tkmedit: Trying to open

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.dat
 surfer: Interpreting overlay volume

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii
 as encoded scalar volume.
 surfer: curvature read: min=-1.094241 max=1.337460
 reading colortable from annotation file...
 colortable with 36 entries read (originally

 /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
 Found embedded color table in annotation.
 8089 vertices did not have an annotation!
 surfer: single buffered window
 surfer: tkoInitWindow(DM)
 Reading mris mask

 /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz
 surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
 Reading /usr/local/freesurfer/tktools/tkm_common.tcl
 Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
 Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /usr/local/freesurfer/tktools/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...
 % ^CKilled
 Area degli allegati
 Visualizza anteprima allegato fieldsign_map.tiff
 Fai clic qui per rispondere o inoltrare il messaggio
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-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] Average myelination within ROI

2014-09-03 Thread SHAHIN NASR

Hi Surfers,

I want to measure the average amount of myelinations within my ROI(s),
I have already generated my myelination maps on surfaces (e.g.
lh.myelin_ProjFrac0p5.nii ).  Then I used mri_segstats as below:

mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum
V1_Stats.txt --accumulate

but the numbers don't make any sense.  For instance:

# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range
  1   012526182573.4  Seg 110280.4453 0.2922-5.5000
51.56.5000
  2   1  1138  764.8  Seg0001   941.0988 0.1572 0.2675
1.4203 1.1527

How can mean=941.0988 when the max=1.4203 ???

Regards
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] bbregister for MRA

2014-08-20 Thread SHAHIN NASR

Hi Surfers
 I want to use bbregister to register my MRA scans to the structural
scans.  The first attempts by using these parameters came out OK but not
perfect:

bbregister --s Subject_ID --mov MRA.nii --init-fsl --reg register.dat
--bold

However,  there are obvious problems around frontal areas.

I have to admit that one of the reasons for this imperfect registration may
be that MRA scans do not cover the whole brain.  However, they still cover
a large portion of it. I was wondering if there is any argument in
bbregister command that may help me improve the quality.  It is very fine
if it increases the registration time.

Regards

P.S.:  using --t2 in bbregister (instead of --bold) generated the same
outcome but --t1 was completely off.
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] mc-bbr

2014-03-27 Thread SHAHIN NASR

Hi,
For a project in which subjects have repeated head movements, I want to
register every TR to anatomical scans separately to reduce the effect of
head movement as much as possible.  When I checked the old posts, I noticed
that there has been a code since 2011 (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.html)
to do this (named mc-bbr).   But I am not sure if it is valid any more and
not sure how does it works.

As far as I see, there is no flag for mc-bbr or something similar to
that in preproc-sess. I appreciate if you guide me through it.

Regards
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] selxavg3-sess error

2014-03-19 Thread SHAHIN NASR

Hopefully this is the last problem with per-run analysis (in native space)
but as far as I see, preproc-sess and selxavg3-sess do not generate

/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat

Because of that, when I use tksurfer-sess it faces an error:

ERROR: cannot find
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat

I can use bbregister to register
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/template.nii.gz
to the subject's anatomical scan and then use the register.dof.dat file for
tksurfer. But is this the correct thing to do?





On Wed, Mar 19, 2014 at 11:41 AM, sha...@nmr.mgh.harvard.edu wrote:

 YES! Started to work.

 Thanks Doug!

  use
  -nuisreg mcprextreg 3
 
  On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote:
  I used -nuisreg mcprextreg in mkanalysis-sess. Got this error:
 
  Error: -nuisreg requires two arguments
 
 
 
  -nuisreg
 
  On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote:
  Does not accept -nuis flag. I changed my mkanalysis-sess to this:
 
  mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5
  -paradigm
  Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis
  mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color
  -per-run
 
  and got this error:
 
  ERROR: Flag -nuis unrecognized.
 
 
 
  I think it is just confused because it expects native to be
  per-session.
  One way around this is to just specify -nuis mcprextreg instead of
  -mcprextreg
  doug
 
 
  On 03/19/2014 11:15 AM, sha...@nmr.mgh.harvard.edu wrote:
  But this is a per-run analysis and preproc-sess is -per-run (in
  native
  space).  I assumed that I have to change my mkanalysis-sess to this:
 
  mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA  -fwhm 1.5
  -paradigm
  Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25
  -mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd
  bold_Color
  -per-run
 
 
  But using -mcprextreg flag generates an error. Is it a bug?
 
 
  There is not an mcextreg file there. There is mcprextreg file. I
  think
  you need to run preproc with -per-session to get the mcextreg file
  doug
 
  On 03/18/2014 02:34 PM, SHAHIN NASR wrote:
  Hi,
When I run selxavg3-sess, I face this error:
 
  ERROR: cannot find volume matching
 
 /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
  ERROR: loading nonpar reg
 
 /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
  --
  ERROR: fast_selxavg3() failed\n
 
   I repeated the preproc-sess from scratch and it worked fine,
  finished without any problem and I still get the same error.  I
  even
  check the registration in this run and it fine.
 
   Now I am wondering why do I see this error for this subjects
  (and
  why I don't see it for the other subjects)?
 
  Regards
  --
  Shahin Nasr
 
  PhD in Cognitive Neuroscience
  Martinos Imaging Center, MGH
  Harvard Medical School
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing:
  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing:
  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing:
  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 
 
 
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
 
 





-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] selxavg3-sess error

2014-03-18 Thread SHAHIN NASR

Hi,
   When I run selxavg3-sess, I face this error:

ERROR: cannot find volume matching
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
ERROR: loading nonpar reg
/autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg
--
ERROR: fast_selxavg3() failed\n

  I repeated the preproc-sess from scratch and it worked fine, finished
without any problem and I still get the same error.  I even check the
registration in this run and it fine.

  Now I am wondering why do I see this error for this subjects (and why I
don't see it for the other subjects)?

Regards
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] per-run and Native space

2014-03-14 Thread SHAHIN NASR

I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with
this command

preproc-sess -fwhm 1.5 -fsd bold -per-run

I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset.
 Although preproc-sess finishes without any error, it only generates
fmcpr.nii.gz and when I run selxavg3-sess, it returns an error that

 cannot determine format of
 test/bold/013/fmcpr.sm1.5

and exits.  Would you tell me why those files are not generated?

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] absolute value of effect size

2014-01-07 Thread SHAHIN NASR

Hi,
I have two related questions.  I have two conditions (e.g. C1 and C2)
and I want to generate a map that shows all voxels that can differentiate
C1 from C2 *irrespective* of whether C1C2 or C1C2.  I think it can be
done easily by:

mris_calc -o sig.nii abs_sig.nii abs

If I am right, then:
1) Can I apply the same command to ces.nii file to have the absolute value
of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other
factors?
2) Do I need to apply the same routine to cesvar?

Thanks
-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] saving in GIFTI .func.gii format

2013-11-08 Thread SHAHIN NASR

Hi Surfers
I have done a surface-based group-averaged mapping and now I need to
save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii
format.  Does mri_glmfit support this output format?

Regards


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] using multiple functional ROIs in fcseed-config

2013-10-10 Thread SHAHIN NASR

Hi,
I know that we can have multiple segments (segIDs) in fcseed-config.
 Is there anyway to use multiple ROIs (functionally defined) in
fcseed-config?
If no, what is the alternative? Is there anyway to average the .dat
output files generated by separate fcseed commands? Is it OK to manually
average the .dat files?  Should we consider anything in this averaging?

Thanks

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Why don't no-mask flag work?

2013-10-03 Thread SHAHIN NASR

This time, selxavg3-sess finished without any error but everything outside
the brain including eyes are cut (for me i.e. failure). Apparently, no-mask
flag is ignored (!). To help you find the problem I copy/paste my commands
here:

preproc-sess -s Sbj_53/abir/ -fwhm 2 -per-session -fsd bold -no-subcort-mask

mkanalysis-sess -analysis RetinaPrj_New  -fwhm 2 -paradigm Conds.par
-native -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000
-nconditions 3 -refeventdur 14 -runlistfile RunList -per-session -fsd bold
-no-subcort-mask -no-mask

selxavg3-sess -s Sbj_53/abir -a RetinaPrj_New

I am also attaching the analysis.info

If you want to test the files, you can see the subject files in:
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir

Note: I did all of these tests from scratch after deleting files from the
previous tests.  So it can't be due to a remaining file from the previous
processes.




On Thu, Oct 3, 2013 at 3:47 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 OK, try it like this using the dev env
 1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask
 2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask

 Note that the eyes may get cut off in the mni305 space. You might just
 want to keep it in native space.

 doug






 On 10/03/2013 03:19 PM, sha...@nmr.mgh.harvard.edu wrote:

 preproc-sess -s SbjName -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask
 -no-subcort-mask

 I also tried per-session and mni305-2mm but still did not help.
 I even tried doing it in native space (by not mentioning mni305/fsaverage)
 but did not work either.


  What was your preproc-sess command?


 On 10/03/2013 10:29 AM, SHAHIN NASR wrote:

 Hi Doug,
  Did you have a chance to find the reason for this problem?


 On Wed, Oct 2, 2013 at 3:20 PM, sha...@nmr.mgh.harvard.edu
 mailto:sha...@nmr.mgh.**harvard.edu sha...@nmr.mgh.harvard.edu
 wrote:

  I still receive the same error message (1mm is now 2mm in the
  message).

  outanadir =
  /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/**
 Sbj_53/abir/bold/RetinaPrj_**nomask2
  Error using MRIread (line 76)
  ERROR: cannot determine format of
  /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/**
 Sbj_53/abir/bold/008/masks/.**mni305.2mm
  (MRIread)


  Error in fast_selxavg3 (line 146)
runmask = MRIread(flac.maskfspec);



   Does the same thing happen if you use the 2mm instead of the 1mm?
  
   On 10/02/2013 02:21 PM, SHAHIN NASR wrote:
   Hi,
   I want to test activity outside the brain (around
  eyes/retina) but
   when I use -no-mask flag in my mkanalysis-sess (to be able to
 see
   activity outside brain) as below:
  
   mkanalysis-sess -analysis RetinaPrj_nomask  -fwhm 2 -paradigm
   Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25
 1.25
   -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force
  -runlistfile
   RunList -per-run -fsd bold -no-mask
  
   I get this error:
  
   outanadir =
  
  /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/**
 Sbj_53/abir/bold/RetinaPrj_**nomask
   Error using MRIread (line 76)
   ERROR: cannot determine format of
  
  /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/**
 Sbj_53/abir/bold/008/masks/.**mni305.1mm
   (MRIread)
  
  
   Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
--**
   ERROR: fast_selxavg3() failed\n
  
   Note:
   ** I have already used -nomask and -no-subcort-mask in the
  preproc-sess
   *** If I remove this flag, everything looks fine except for the
  fact
   that all activity outside brain is masked!
  
  
   --
   Shahin Nasr
  
   PhD in Cognitive Neuroscience
   Martinos Imaging Center, MGH
   Harvard Medical School
  
  
   --
   Douglas N. Greve, Ph.D.
   MGH-NMR Center
   gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 
   Phone Number: 617-724-2358 tel:617-724-2358
   Fax: 617-726-7422 tel:617-726-7422
  
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[Freesurfer] Why don't no-mask flag work?

2013-10-02 Thread SHAHIN NASR

Hi,
I want to test activity outside the brain (around eyes/retina) but when
I use -no-mask flag in my mkanalysis-sess (to be able to see activity
outside brain) as below:

mkanalysis-sess -analysis RetinaPrj_nomask  -fwhm 2 -paradigm Conds.par
-mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000
-nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd
bold -no-mask

I get this error:

outanadir =
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm
(MRIread)


Error in fast_selxavg3 (line 146)
  runmask = MRIread(flac.maskfspec);

 --
ERROR: fast_selxavg3() failed\n

Note:
** I have already used -nomask and -no-subcort-mask in the preproc-sess
*** If I remove this flag, everything looks fine except for the fact that
all activity outside brain is masked!


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] cvs_avg35

2013-07-28 Thread SHAHIN NASR

Hi,
Would you tell me where I can find cvs_avg35 brain template.


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-24 Thread SHAHIN NASR

Hi Doug,
Sorry to follow this topic with a delay but we tried to model BOLD
signal undershoot with a gamma function and we failed. The problem is,
gamma function generates positive values and we can NOT use inverse gamma
function (or otherfunction similar to that) as a part of mkanalysis-sess
(for modeling BOLD signal undershoot). We even used matlab gammafit to
estimate parameters and it said that values should be positive otherwise
gammafit function fails.
Do you have any suggestion?

On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

yes, that is what you want. The only other way that comes to mind is to
model each event type as two event types one delayed relative to the other.
Then model the responseto each as a gamma. If the delay is right, then the
first gamma should model the main positive response and the second gamma
will model the negative response. both will be independent from the other.

doug

On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:

I think I figured it out but I want to double check. I am generating
group-average map for my subjects using isxconcat-sess command which
generates ces maps for each time frame. I think these maps are what I
wanted. Right?
If you still have other solutions that you think may generate more
reliable results, I am eager to know. For instance, is there anyway to
fit a model as we do for spmhrf or fslhrf, but just for the negative
peak?

Regards

That's the problem Doug. I have already generated the FIR model but how
can
I show the sig MAP for one particulat time point. What are the other
ways?

On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu**wrote:

Hi Shahin, there are several ways that you could do it. The one that
immediately comes to mind is to use an FIR and then test for a
difference
at a particular post stimulus time point.
doug

On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

Hi,
I want to generate a map to show the significant difference
between
HRF undershoot (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this
map?

P.S.: Please note that I need a map and not a time course graph.

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-11 Thread SHAHIN NASR

Sorry that I keep on asking questions but I want to know if using a model
can significantly increase the chance of getting a significant response.
As far as I see for the positive peak, when I use a model (e.g. gamma
model or spmhrf), I see a more significant response compared to when I use
the FIR model. Is it correct? If true, then the same might be correct for
the negative peak.

P.S.: To be more clear, I am talking about the response maps relative to
the baseline.
On Apr 10, 2013 6:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:

doug

On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:

Regards

That's the problem Doug. I have already generated the FIR model but how
can
I show the sig MAP for one particulat time point. What are the other
ways?

On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu**wrote:

Hi Shahin, there are several ways that you could do it. The one that
immediately comes to mind is to use an FIR and then test for a
difference
at a particular post stimulus time point.
doug

On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

P.S.: Please note that I need a map and not a time course graph.

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Shahin Nasr

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Comparing HRF undershoots between conditions

2013-04-10 Thread SHAHIN NASR

Hi,
 I want to generate a map to show the significant difference between
HRF undershoot  (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this map?

P.S.: Please note that I need a map and not a time course graph.


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-10 Thread SHAHIN NASR

That's the problem Doug. I have already generated the FIR model but how can
I show the sig MAP for one particulat time point. What are the other
ways?

On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

Hi Shahin, there are several ways that you could do it. The one that
immediately comes to mind is to use an FIR and then test for a difference
at a particular post stimulus time point.
doug

On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

Hi,
I want to generate a map to show the significant difference between
HRF undershoot (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this map?

P.S.: Please note that I need a map and not a time course graph.

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Shahin Nasr

[Freesurfer] selxavg3-sess problem with -per-run flag

2013-03-29 Thread SHAHIN NASR

Hi,
 I used to run my mkanalysis-sess without indicating -per-run or
-per-session, assuming that when I have pre-processed my files with
-per-run flag then selxavg3-sess will do the same. But when I checked the
analysis.info I noticed  PerSession 1 which I think it means system will
use per-session preprocessing. So, this time I explicitly used -per-run in
my mkanalysis-sess as below:

preproc-sess -s SubjId -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self rhlh

mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5
-paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg
-TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force

This time when I ran selxavg3-sess command I faced this error:

ERROR: cannot determine format of
/autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5
(MRIread)


Error in flac_customize (line 87)
mri = MRIread(fstem,1);

Error in fast_selxavg3 (line 65)
flac0 = flac_customize(flac0);

 --
ERROR: fast_selxavg3() failed\n


As I checked my subjects directory I had these files in /bold/004/
directory:

fmcpr.nii.gz
fmcpr.sm5.self.rh.nii.gz
fmcpr.sm5.self.lh.nii.gz

Notably, if I drop that -per-run flag from my mkanalysis-sess then system
works without any problem. But then I am not sure whether I have processed
my data in per-run or per-session mode.

Any help will be appreciated
Regards


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

2012-10-24 Thread SHAHIN NASR

Thanks doug But I am not sure if it was the answer. To be more specific, my
subjects did two different tasks within one fmri run. I want to see their
functional connectivity during task 1 and task 2 separately.

If it was resting state, I didn't need to separate my data and a simple
fcseed-config like below was enough:

fcseed-config -roi Labels/rh.V1 -fcname mean.R_V1.dat -fsd rest -mean -cfg
CFG_Files/mean.R_V1.config

But now, I don't know how to modify my fcseed-config to say I have had two
conditions (task) within one run and I need to measure the seed for each
task separately.

On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

Hi Shahin, you can do seed-based analysis. In principle you can do this
with task data, you just need to adjust your conclusions accordingly. There
is no easy to way to only do the analysis on the resting epochs of a
blocked design, if that is what you mean.
doug

On 10/24/2012 12:55 AM, SHAHIN NASR wrote:

Hi,

I was wondering if we can compare functional connectivity between
blocks within a run as we do for BOLD signal using freesurfer. Current
documentation of freesurfer is for resting state and does not consider
conditions that experiment is Blocked Design.

Similar question has been asked previous but nobody answered (see the
link below)
https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2012-**
June/024394.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html

Regards

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

--
Shahin Nasr

[Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

2012-10-23 Thread SHAHIN NASR

Hi,

   I was wondering if we can compare functional connectivity between
blocks within a run as we do for BOLD signal using freesurfer. Current
documentation of freesurfer is for resting state and does not consider
conditions that experiment is Blocked Design.

Similar question has been asked previous but nobody answered (see the link
below)
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] Non rigid registration

2012-07-30 Thread SHAHIN NASR

Hi,

  In our functional MRI studies, we co-registration the functional
images to anatomical scans (a part of preproc-sess routine in version 5)
before measuring the contrasts. But for one of our studies, a reviewer has
asked if a “non-rigid image registration” would change results when we are
assessing activity within artifact-prone brain areas (e.g. anterior
temporal areas).

  As far as I know, freesurfer registration works fine and even in this
study, we have found very strong activity/contrast within anterior tempotal
lobe.  But I was wondering whether you have tested this possibility or not.
If yes, then I appreciate if you can introduce me a reference (published
article) to support our answer.

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Recent paper on FreeSurfer reliability

2012-06-20 Thread SHAHIN NASR

Please post it on PLoS One homepage. According to the policies of this
journal, you are allowed to respond to each paper directly on the same page
as the article. You don't need to submit it as a paper and won't go through
a review process.



On Wed, Jun 20, 2012 at 10:28 AM, Peter J. Molfese 
pmolf...@haskins.yale.edu wrote:

 We run things on an Xgrid cluster that is now a mixture of Macs running
 Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from
 asegstats2table and aparcstats2table are identical after running 100
 subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1.  I also
 ran a few subjects on the cluster and on individual computers (not on the
 cluster so to speak) and the results are identical.

 Best,
 Peter


 Hi,

 The paper entitled

 “The Effects of FreeSurfer Version, Workstation Type,
 and Macintosh Operating System Version on Anatomical
 Volume and Cortical Thickness Measurements”,
 PLoSONE, Vol 7(6), e38234 (2012)

 may be of interest to all of you. It can be found at:
 http://dx.plos.org/10.1371/journal.pone.0038234

 Cheers,
 Ed



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PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] averaging sessions with different TRs

2012-06-09 Thread SHAHIN NASR

Hi,
 I was wondering if I can average two scan sessions with different TRs
or not. Number of conditions and all other factors are exactly the same
between the two sessions.

regards
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[Freesurfer] Per-run registration in monkey fmri

2012-01-20 Thread SHAHIN NASR

Hi
   In monkey fmri, we usually have to do the functional-anatomical
registration manually since bbregister doesn't work very well.
It was easy in version 4.5 since we usually used just one run for
registration.  In version 5.1 we can use per-run option to improve
registration but I am wondering how can we use it in monkey fmri? Should we
register each run separately? Then how can we combine those individual
registration files to generate the final registration file.
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[Freesurfer] Selxavg3-sess Out of Memory - What are the options?

2012-01-11 Thread SHAHIN NASR

Hi,

I am running selxavg3-sess under freesurfer 4.5 and I faced out of
memory error as it started computing whitening matrices. Since they are
monkey datasets, runs were relatively long (12 runs each 16 min; TR=1.4). I
want to know what options do I have here? Please note that, when I applied
this command to 3 runs rather than all 12 runs (by making a runlist), I
didn't face this error.

P.S.: I can not use version 5.1 because we don't have structural scan for
this monkey and we just want to check the functional scans without any
registration.  I assume it is not possible in version 5.

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Event-Related design and jitter in stimulus onset

2011-12-09 Thread SHAHIN NASR

Thanks Doug.
In my experiment, each trial (event) consists of 1 sec stimulus
presentation and 5 sec blank interval (TR=2). I have also added a condition
with just blank presentation which will be repeated as much as other events.

I have used optseq2 commands to generate the trial sequence. But I
faced two problem/questions:

1) Using this command, I expected to see a Null event (other than my
blank condition) with variable length (irrespective of TR) between other
trials. But to my surprise, length of the Null event was always a
multiplication of TR. Is that correct?
2) Also, for psdmin psdmax I wasn't sure if they are number of TRs or
number of seconds and what is a safe window length when my stimuli are very
simple visual objects (and no cognitive task).

Once again, thanks for your help.

On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

Hi Shahin, there are several ways to answer this question. If you are
going to analyze assuming a shape to the HRF, then the actual delay between
stimuli is technically not important (though 4s will be good to avoid
attenuation in the following stimulus). If you're using an FIR model of the
HRF (no assumed shape), then I usually advise that you have, in total, as
much time spent on fixation (or whatever your null stimulus is) as you have
for any other stimulus. You can use optseq to compute the actual schedule.
doug

SHAHIN NASR wrote:

Hi Surfers,

It is my first experience with Event-related paradigms. In my
experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum
variable delay between trials to be able to analyze data without any
confound.

Regards

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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[Freesurfer] Event-Related design and jitter in stimulus onset

2011-12-08 Thread SHAHIN NASR

Hi Surfers,

   It is my first experience with Event-related paradigms. In my
experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum
variable delay between trials to be able to analyze data without any
confound.

Regards

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR

Hi,

 I have generated two different functional connectivity maps for two
different ROI-based seeds. These maps are based on group-average of the same
subjects (generated by using separate isxconcat-sess commands ), and now I
want to see the difference map. To do so, I used mris_calc as below.

 mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub   map2/rh.ces.nii

Also, to generate the rh.cesvar.nii file I used this command:

 mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii   sub
map2/rh.cesvar.nii

But then when I used the glmfit with WLS option as below:

 mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask
../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf
fsaverage rh --wls rh.cesvar.nii

 I faced an error saying: Error: MRInormWeights: values less than or eq to
0 which I assumed is related to an error in rh.cesvar.nii file (am I
right?). Would you tell me how can I fix this problem?

P.S.: please note that sequence of subjects and all MRI parameters are
exactly the same between the two maps.

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR

Thanks Doug. Just one related question. Should I also generate a new
ffxdof.dat file for this map? I assumed that ffxdof depends on the number of
subjects (session) and since number of subjects (sessions) is the same
between the two groups then I can use those values, generated by
isxconcat-sess for either map1 or map2. Right?

On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

Hi Shahin, it is not as simple as doing a subtraction of the cesvar files.
What you are trying to get is the expected variance of your difference
between the ces files (as a variance, it must be positive). To get this you
need

cesvardiff = (cesvar1+cesvar2)/(2^2)

The 2^2 is the number of inputs (2) squared.

doug

SHAHIN NASR wrote:

Hi,

I have generated two different functional connectivity maps for two
different ROI-based seeds. These maps are based on group-average of the same
subjects (generated by using separate isxconcat-sess commands ), and now I
want to see the difference map. To do so, I used mris_calc as below.
mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub
map2/rh.ces.nii

Also, to generate the rh.cesvar.nii file I used this command:
mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub
map2/rh.cesvar.nii

But then when I used the glmfit with WLS option as below:

mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask
../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf
fsaverage rh --wls rh.cesvar.nii

I faced an error saying: Error: MRInormWeights: values less than or eq
to 0 which I assumed is related to an error in rh.cesvar.nii file (am I
right?). Would you tell me how can I fix this problem?

P.S.: please note that sequence of subjects and all MRI parameters are
exactly the same between the two maps.

--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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Re: [Freesurfer] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR

Do you suggest using random-effect model? Is there any problem with using a
fix-effect model (other than the fact that by using this model we can not
predict response of subjects outside our population)?

On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 It should be roughly the sum of the dofs of the individual subjects. Why
 are you using a fixed-effects model?
 doug

 SHAHIN NASR wrote:

   Thanks Doug. Just one related question. Should I also generate a new
 ffxdof.dat file for this map? I assumed that ffxdof depends on the number of
 subjects (session) and since number of subjects (sessions) is the same
 between the two groups then I can use those values, generated by
 isxconcat-sess for either map1 or map2. Right?



 On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

Hi Shahin, it is not as simple as doing a subtraction of the
cesvar files. What you are trying to get is the expected variance
of your difference between the ces files (as a variance, it must
be positive). To get this you need

cesvardiff = (cesvar1+cesvar2)/(2^2)

The 2^2 is the number of inputs (2) squared.

doug


SHAHIN NASR wrote:

Hi,

 I have generated two different functional connectivity maps
for two different ROI-based seeds. These maps are based on
group-average of the same subjects (generated by using
separate isxconcat-sess commands ), and now I want to see the
difference map. To do so, I used mris_calc as below.
 mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub
  map2/rh.ces.nii

Also, to generate the rh.cesvar.nii file I used this command:
  mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii
  sub   map2/rh.cesvar.nii

But then when I used the glmfit with WLS option as below:

 mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls
--nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii
--ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii

 I faced an error saying: Error: MRInormWeights: values less
than or eq to 0 which I assumed is related to an error in
rh.cesvar.nii file (am I right?). Would you tell me how can I
fix this problem?

P.S.: please note that sequence of subjects and all MRI
parameters are exactly the same between the two maps.

-- Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School


-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
tel:617-726-7422

Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

 http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 




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 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html




-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] funcroi-table-sess with multiple contrasts

2011-10-04 Thread SHAHIN NASR

Hi,

Is there anyway to print multiple contrasts in one output file using
funcroi-table-sess command?

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] using isxconcat for partial correlation coefficient map

2011-09-26 Thread SHAHIN NASR

Hi,

Would you tell me how can I use isxconcat-sess to calculate group
averaged partial correlation coefficient map? I have already generated
pcc.nii files for each individual subject.


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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[Freesurfer] Partial brain scanning and registeration

2011-09-20 Thread SHAHIN NASR

Hi
  I want to know if there is any limit for the automatic registration of
functional scans on structural ones when we are scanning activity  just in
a specific part of the brain (e.g. occipital cortex).
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[Freesurfer] Problem with fcseed-config and fcseed-sess

2011-09-06 Thread SHAHIN NASR

Hi,

I have faced a problem using ROI-based, fcseed-config and fcseed-sess

I used either:

fcseed-config -roi
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/atou_anat/label/rh.V1.label
-fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config

OR:

fcseed-config -roi
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/fsaverage/label/rh.V1.label
-fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config

to generated the mean.R_V1.config file for right V1 area (ROI for V1 is
generated automatically and I have not changed it). Then I use below command
to generate mean.R_V1.dat for the session of interest (e.g. atou)

fcseed-sess -s atou -cfg mean.R_V1.config -make-mask

but I just get a if: Expression Syntax. message and the expected dat file
is not generated.

Do you have any idea what is wrong? Any help will be highly appreciated.

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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