Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   Just as a followup through my reading i've come across posts which use
qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
cortical thickness analysis I would like to smooth all of my
rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
group analysis.  After finding regions of difference, I would then like to
use the ROI to extract each individual's mean thickness in the ROI in order
to run a correlation with other measures.  Based on this, I assume it would
make sense to use smoothed data to identify the ROI and then use unsmoothed
data for extracting actual thickness measures (does lh.thickness.fsaverage
contain the original thickness or warped thickness values).

I am unsure which smoothing is the most accurate or preferred.  In using
qcache the smoothness of the images do not seem to reach the filter level
(based on the earlier email) so I am not sure if there is a freesurfer tool
to check the smoothness level or if the qcache smoothness levels make sense
for cortical thickness.

Thanks,
Ajay

On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache option and
> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
> and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
> to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the smoothness is
> 15mm when calculating monte carlo corrections?  Would there be a different
> way to estimate this since my smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
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[Freesurfer] Stats for Yeo and Choi Parcellations

[Bronwyn Overs]

Hi Freesurfer Mailing List,

I wish to extract stats for my sample for the Yeo 2011 cortical 
parcellations and the Choi 2012 striatal parcellations (7 networks) that 
are provided for download on the freesurfer wiki. My questions are as 
follows:


1. I noticed that the Yeo 2011 annot files are already available in 
fsaverage/label. How do I map these annot file to each of my subjects so 
that I can extract stats?
2. For the Choi 2012 files I wish to use 
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How 
do I map this file to each of my subjects so that I can extract stats 
for the 7Network parcellation?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


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Re: [Freesurfer] Extracting BOLD from a flattened surface

[Taha Abdullah]

Hello Doug,

Sorry for the confusing and long email, I am interested in extracting the
raw BOLD signal from a processed 4D nifit file. After registering the
functional to ${subject}/mri/orig.mgz and generating the registration file,
I proceeded to convert the functional image to the same dimensions as
the lh.inflated surface via mri_vol2surf so the functional data image now
has 127000 x 1 x 1 x 240. So I ran mri_segstats command to extract the bold
signal, but I ended up having 240 rows and 1 column in the text file...the
ultimate goal is to quantify the wave propagation of the BOLD time series
across a flattened patch. Any advice would be greatly appreciated.

Thanks!

On Wed, May 4, 2016 at 2:26 PM, Douglas N Greve 
wrote:

>
> Sorry, can you tell me what you are trying to do? You just want a number
> of time points -by- number of vertices file? Then mri_vol2surf should do
> that for you. Flattening is irrelevant for this as it only changes the
> xyz coordinate of the vertex and not the vertex identity.
> doug
>
>
> On 04/29/2016 11:24 AM, Taha Abdullah wrote:
> > Hello Freesurfer Experts,
> >
> > Long story short--I would like to extract BOLD values from each TR
> > across all vertices for one subjects flattened surface
> > Following is a brief overview of my steps and at the end you can see
> > where I am stuck.
> > First, after */recon-all /I* followed the steps to cut the lh inflated
> > surface, saved as a patch, ran /*mris_flatten, */converted patch into
> > asc file.
> > Second, I used read_patch.m to extract all spatial information and a
> > net loss of approximately 10k vertices (127k to 116k)
> >
> > We had all functional images processed in FSL, the 4D file has
> > 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered
> > the functional and anatomicals together via the following cmd:
> > */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold
> > --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a
> > surface using the following cmd*/: mri_vol2surf --mov
> > filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp
> > trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are
> > 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer
> > cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay
> > /lh.func.vol2surf.mgh/  -timecourse lh.func.vol2surf.mgh;/* click on
> > the patch and shows the timecourse for that selected vertex. Using the
> > View>Configure>overlay I can shuffle through the TRs to inspect the
> > change in raw BOLD signal per vertex.
> >
> > I have been perusing the email web server searching for how to extract
> > the hemodynamic waveform for each vertex across the flattened surface
> > and ultimately will be using matlab to understand how the spatial
> > transformation is happening. As well I have all the matlab files that
> > seemed relevant to my query (read_surf.m, read_patch.m, and
> > readMRI.m). I was hoping that I would be able to have a text file with
> > all the vertices (127K not the flattened 116k) in rows and each column
> > would have the TRs; I ran this command;*/ mri_segstats --slabel
> > cbp001_v1 lh
> > /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label
> > --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh/*, output was the
> > 240 TRs as rows and seems like the average global BOLD signal in the
> > single column corresponding with each TR. Excuse my naiveness, I just
> > recently (1 month ago) started using freesurfer and I feel like I have
> > exhausted as much of the information available on the FS wiki and
> > email server. Any information or advice would be great! I put the
> > commands just to give an idea of my workflow (most of the command
> > lines are from the email server or the FS Wiki) and if there are any
> > issues with my steps please let me know so I can correct them before
> > starting the group analysis.
> >
> > Best,
> > Taha
> >
> > --
> > Taha Abdullah
> > Department of Physiology
> > Northwestern University
> > Masters of Science Physiology and Biophysics, Georgetown University 2015
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this 

Re: [Freesurfer] no recon button

[Bruce Fischl]

Hi Sarah

no, I don't think it is. The recon edit for example will set voxels to 
"1" not "0" when erase so that we can keep track of them. If you are 
editing as part of the recon-all stream you are better off using it than 
just plain voxel editing.

cheers
Bruce
On Wed, 4 May 2016, Burke,Sarah E wrote:

> Douglas, can you please let me know if the voxel edit button is appropriate 
> to use in place of the recon edit?
>
> Thanks,
>
> Sarah
>
> Sent from my iPhone
>
>> On May 3, 2016, at 3:04 PM, Burke,Sarah E  wrote:
>>
>>
>> Is this information correct?
>>
>>> On May 2, 2016, at 3:55 PM, Burke,Sarah E  wrote:
>>>
>>> https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: Monday, May 2, 2016 3:49 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] no recon button
>>>
>>> Can you send us a link to the email you are speaking about?
>>>
 On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
 It opens a box that says "voxel edit" This allows me to edit the images 
 accordingly, however I read in the email forum that this may create some 
 issues further on down the line?

 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Douglas N Greve 
 
 Sent: Monday, May 2, 2016 3:26 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] no recon button

 what happens when you click on the button with the pencil in it? The one
 just above the "S" in "Surfaces"

> On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas Greve
> 
> *Sent:* Monday, May 2, 2016 2:31 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] no recon button
> Can you send a snapshot of your Freeview window? The Recon Edit button
> looks like a sagittal slice with an "R" in it and a pencil pointing to it.
>
>> On 5/2/16 1:44 PM, Burke,Sarah E wrote:
>> Thank you Douglas. However, in the tutorial for editing output, it
>> says to use the recon edit button to manually perform edits. After
>> this step, I use the command line and recon-all. How do I do the
>> manual edits without this button. I do see a voxel edit button.
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
>>
>> 
>>
>> FsTutorial/PialEdits_freeview - Free Surfer Wiki
>> 
>> surfer.nmr.mgh.harvard.edu
>> top | previous Correcting Pial Surfaces. To follow this exercise
>> exactly be sure you've downloaded the tutorial data set before you
>> begin. If you choose not to ...
>>
>>
>>
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  on behalf of Douglas Greve
>> 
>> *Sent:* Monday, May 2, 2016 1:29 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] no recon button
>> freeview does not have a recon button. You have to run recon-all from
>> the command line.
>>
>>> On 5/2/16 12:14 PM, Burke,Sarah E wrote:
>>> Hello,
>>>
>>>
>>> I searched the mail list and saw that others have had this problem,
>>> but I see no answers to their queries. I have version 1.0
>>> (5/13/2013) of Freeview for Linux.  I have no recon button. What
>>> should I do?
>>>
>>>
>>> Thank you
>>>
>>>
>>>
>>> ___
>>> 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
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: 

[Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and
mris_fwhm and which is appropriate for a cortical thickness analysis.  I
processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
(converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
and 20mm it was approximately 9.3-9.9 smoothness level.

I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
using SurfFWHM on the smae subject the smoothness was estimated at 11.25.


1) I am not sure if the qcache or the mris_fwhm file is more appropriate to
use for a cortical thickness analysis.

2) For qdec if I select the 15mm  option does it assume the smoothness is
15mm when calculating monte carlo corrections?  Would there be a different
way to estimate this since my smoothness at 15mm is closer to 10mm?

Thanks,
Ajay
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[Douglas N Greve]

I think I have a fix for this if you want to edit your version of 
fast_selxavg3.m

Change this line:

if(~isempty(analysis) & DoGLMFit & strcmp(flac.designtype,'event-related'))

To:

% Check to make sure that each task ev as the same number
% of regressors before saving the h.dat file
evtaskind = flac_evtaskind(flac0);
% number of regressors in each ev
nregperev = zeros(length(evtaskind),1);
for n = 1:length(evtaskind)
   nregperev(n) = flac0.ev(evtaskind(n)).nreg;
end
nregperevunique = length(unique(nregperev));

if(~isempty(analysis) & DoGLMFit & nregperevunique==1 & 
strcmp(flac.designtype,'event-related'))




On 05/04/2016 04:08 PM, S.V.Shepherd [work] wrote:
> I can /also /confirm that it ran fine when the big matrix was changed 
> from taskreg to nuisreg, so we can probably consider the issue 
> resolved. I suspect the problem is with multi-column taskregs.  If I 
> want to have the regressors tracked equivalently across runs, I'd need 
> to add them as taskregs, one column per file.
>
> Just to confirm: There's no way to visualize the nuisreg 
> loadings/maps, right?
>
> stephen
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 
> USA // 212.327.7699 
>
> On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] 
> > 
> wrote:
>
> I can confirm that having taskregs with a paradigm works. For
> example, I've run successfully analyzed the following:
>
> mkanalysis-sess  -native  -event-related  -refeventdur 10 
> -paradigm aboutFace.para  -nconditions 13  -TR 2.  -rlf
> rlf_aboutFace_subjvid  -funcstem fm2tas1 -mask brain  -analysis
> a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg
> taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1 
> -fsd bold  -gammafit 0 8 -gammaexp 0.3  -polyfit 2  -acfbins 1 
> -nuisreg motion.dat 3  -force
>
> The only thing that's changed is the addition of the IC-derived
> taskreg matrix.
>
> stephen
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York
> NY 10065-6307 USA // 212.327.7699 
>
> On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve
> > wrote:
>
> I don't think it is going to work to have both a -taskreg and a
> paradigm. You should be able to model it as a nuisance
> regressor. The
> fact that it may be the same across runs won't make much of a
> difference.
> doug
>
> On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote:
> > mkanalysis-sess  -native  -event-related -refeventdur 10 
> -paradigm
> > aboutFace.para  -nconditions 13  -TR 2. -rlf
> > rlf_aboutFace_subjvid  -funcstem fm2tas1 -mask brain -analysis
> > a_401_Av_s_task_fmov_bgrnd_icadenoise -taskreg
> > taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1
> > -taskreg noisereg__TCs_Milo_43.dat 43 -fsd bold -gammafit 0 8
> > -gammaexp 0.3  -polyfit 2  -acfbins 1 -nuisreg motion.dat 3 
> -force
> >
> > I've attached example noisereg__TCs_Milo_43.dat and a log
> which I
> > think includes relevant terminal outputs up to the error.
> Please let
> > me know if I should provide more information.
> >
> > s
> >
> >
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY
> 10065-6307
> > USA // 212.327.7699 
> >
> > On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve
> >  
>  >> wrote:
> >
> > Can you send your mkanalysis-sess command? Can you also
> send one
> > of the
> > regressor files? And can you send the full selxavg3
> terminal output?
> >
> > On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> > > I've modified an analysis to include a vector of noise
> time courses
> > > estimated using ICA. Since IC effects should be
> consistent across
> > > runs, I'm using taskregs instead of nuisregs. I can
> define the
> > > analysis and set up contrasts fine; however, when I
> run the analysis
> > > (selxavg3-sess), I get the following error:
> > >
> > > [...]
> > > Saving h.dat to
> > >
> >
>  
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> > > Error using zeros
> > > Size inputs must be integers.
> > >
> > > Error in 

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[Douglas N Greve]

On 05/04/2016 04:08 PM, S.V.Shepherd [work] wrote:
> I can /also /confirm that it ran fine when the big matrix was changed 
> from taskreg to nuisreg, so we can probably consider the issue 
> resolved. I suspect the problem is with multi-column taskregs.  If I 
> want to have the regressors tracked equivalently across runs, I'd need 
> to add them as taskregs, one column per file.
Can you send me the Xtmp.mat file from a run that fails?
>
> Just to confirm: There's no way to visualize the nuisreg 
> loadings/maps, right?
right
>
> stephen
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 
> USA // 212.327.7699 
>
> On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] 
> > 
> wrote:
>
> I can confirm that having taskregs with a paradigm works. For
> example, I've run successfully analyzed the following:
>
> mkanalysis-sess  -native  -event-related  -refeventdur 10 
> -paradigm aboutFace.para  -nconditions 13  -TR 2.  -rlf
> rlf_aboutFace_subjvid  -funcstem fm2tas1 -mask brain  -analysis
> a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg
> taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1 
> -fsd bold  -gammafit 0 8 -gammaexp 0.3  -polyfit 2  -acfbins 1 
> -nuisreg motion.dat 3  -force
>
> The only thing that's changed is the addition of the IC-derived
> taskreg matrix.
>
> stephen
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York
> NY 10065-6307 USA // 212.327.7699 
>
> On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve
> > wrote:
>
> I don't think it is going to work to have both a -taskreg and a
> paradigm. You should be able to model it as a nuisance
> regressor. The
> fact that it may be the same across runs won't make much of a
> difference.
> doug
>
> On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote:
> > mkanalysis-sess  -native  -event-related -refeventdur 10 
> -paradigm
> > aboutFace.para  -nconditions 13  -TR 2. -rlf
> > rlf_aboutFace_subjvid  -funcstem fm2tas1 -mask brain -analysis
> > a_401_Av_s_task_fmov_bgrnd_icadenoise -taskreg
> > taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1
> > -taskreg noisereg__TCs_Milo_43.dat 43 -fsd bold -gammafit 0 8
> > -gammaexp 0.3  -polyfit 2  -acfbins 1 -nuisreg motion.dat 3 
> -force
> >
> > I've attached example noisereg__TCs_Milo_43.dat and a log
> which I
> > think includes relevant terminal outputs up to the error.
> Please let
> > me know if I should provide more information.
> >
> > s
> >
> >
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY
> 10065-6307
> > USA // 212.327.7699 
> >
> > On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve
> >  
>  >> wrote:
> >
> > Can you send your mkanalysis-sess command? Can you also
> send one
> > of the
> > regressor files? And can you send the full selxavg3
> terminal output?
> >
> > On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> > > I've modified an analysis to include a vector of noise
> time courses
> > > estimated using ICA. Since IC effects should be
> consistent across
> > > runs, I'm using taskregs instead of nuisregs. I can
> define the
> > > analysis and set up contrasts fine; however, when I
> run the analysis
> > > (selxavg3-sess), I get the following error:
> > >
> > > [...]
> > > Saving h.dat to
> > >
> >
>  
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> > > Error using zeros
> > > Size inputs must be integers.
> > >
> > > Error in fast_selxavg3 (line 1248)
> > >   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; %
> Add zero
> > for cond 0
> > >
> > > >> --
> > > ERROR: fast_selxavg3() failed\n
> > > a_401_Av_s_task_fmov_bgrnd_icadenoise failed
> > > [...]
> > >
> > > 
> > >
> > > Looking at h.dat, I notice "Nh" is set 3.625000e+00
> rather than
> > "1" as

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

I can *also *confirm that it ran fine when the big matrix was changed from
taskreg to nuisreg, so we can probably consider the issue resolved. I
suspect the problem is with multi-column taskregs.  If I want to have the
regressors tracked equivalently across runs, I'd need to add them as
taskregs, one column per file.

Just to confirm: There's no way to visualize the nuisreg loadings/maps,
right?

stephen

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699

On Wed, May 4, 2016 at 3:40 PM, S.V.Shepherd [work] <
stephen.v.sheph...@gmail.com> wrote:

> I can confirm that having taskregs with a paradigm works. For example,
> I've run successfully analyzed the following:
>
> mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
> aboutFace.para  -nconditions 13  -TR 2.  -rlf rlf_aboutFace_subjvid
> -funcstem fm2tas1  -mask brain  -analysis
> a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg taskreg_face__zmove.dat 1
> -taskreg taskreg_face__bgrnd.dat 1  -fsd bold  -gammafit 0 8  -gammaexp
> 0.3  -polyfit 2  -acfbins 1  -nuisreg motion.dat 3  -force
>
> The only thing that's changed is the addition of the IC-derived taskreg
> matrix.
>
> stephen
>
> *stephen v. shepherd   phd*
> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
> // 212.327.7699
>
> On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve  > wrote:
>
>> I don't think it is going to work to have both a -taskreg and a
>> paradigm. You should be able to model it as a nuisance regressor. The
>> fact that it may be the same across runs won't make much of a difference.
>> doug
>>
>> On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote:
>> > mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
>> > aboutFace.para  -nconditions 13  -TR 2. -rlf
>> > rlf_aboutFace_subjvid  -funcstem fm2tas1  -mask brain -analysis
>> > a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg
>> > taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1
>> > -taskreg noisereg__TCs_Milo_43.dat 43  -fsd bold -gammafit 0 8
>> > -gammaexp 0.3  -polyfit 2  -acfbins 1 -nuisreg motion.dat 3  -force
>> >
>> > I've attached example noisereg__TCs_Milo_43.dat and a log which I
>> > think includes relevant terminal outputs up to the error. Please let
>> > me know if I should provide more information.
>> >
>> > s
>> >
>> >
>> >
>> > _stephen v. shepherd   phd_
>> > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
>> > USA // 212.327.7699
>> >
>> > On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve
>> > > wrote:
>> >
>> > Can you send your mkanalysis-sess command? Can you also send one
>> > of the
>> > regressor files? And can you send the full selxavg3 terminal output?
>> >
>> > On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
>> > > I've modified an analysis to include a vector of noise time
>> courses
>> > > estimated using ICA. Since IC effects should be consistent across
>> > > runs, I'm using taskregs instead of nuisregs. I can define the
>> > > analysis and set up contrasts fine; however, when I run the
>> analysis
>> > > (selxavg3-sess), I get the following error:
>> > >
>> > > [...]
>> > > Saving h.dat to
>> > >
>> >
>>  
>> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
>> > > Error using zeros
>> > > Size inputs must be integers.
>> > >
>> > > Error in fast_selxavg3 (line 1248)
>> > >   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero
>> > for cond 0
>> > >
>> > > >> --
>> > > ERROR: fast_selxavg3() failed\n
>> > > a_401_Av_s_task_fmov_bgrnd_icadenoise failed
>> > > [...]
>> > >
>> > > 
>> > >
>> > > Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than
>> > "1" as
>> > > usual.
>> > >
>> > > Any tips on how to debug further?
>> > >
>> > > _stephen v. shepherd   phd_
>> > > The Rockefeller University / 1230 York Avenue / New York NY
>> 10065-6307
>> > > USA // 212.327.7699 
>> > >
>> > >
>> > > ___
>> > > 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
>> > 

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

I can confirm that having taskregs with a paradigm works. For example, I've
run successfully analyzed the following:

mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
aboutFace.para  -nconditions 13  -TR 2.  -rlf rlf_aboutFace_subjvid
-funcstem fm2tas1  -mask brain  -analysis
a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg taskreg_face__zmove.dat 1
-taskreg taskreg_face__bgrnd.dat 1  -fsd bold  -gammafit 0 8  -gammaexp
0.3  -polyfit 2  -acfbins 1  -nuisreg motion.dat 3  -force

The only thing that's changed is the addition of the IC-derived taskreg
matrix.

stephen

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699

On Wed, May 4, 2016 at 3:39 PM, Douglas N Greve 
wrote:

> I don't think it is going to work to have both a -taskreg and a
> paradigm. You should be able to model it as a nuisance regressor. The
> fact that it may be the same across runs won't make much of a difference.
> doug
>
> On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote:
> > mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
> > aboutFace.para  -nconditions 13  -TR 2. -rlf
> > rlf_aboutFace_subjvid  -funcstem fm2tas1  -mask brain -analysis
> > a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg
> > taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1
> > -taskreg noisereg__TCs_Milo_43.dat 43  -fsd bold -gammafit 0 8
> > -gammaexp 0.3  -polyfit 2  -acfbins 1 -nuisreg motion.dat 3  -force
> >
> > I've attached example noisereg__TCs_Milo_43.dat and a log which I
> > think includes relevant terminal outputs up to the error. Please let
> > me know if I should provide more information.
> >
> > s
> >
> >
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
> > USA // 212.327.7699
> >
> > On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve
> > > wrote:
> >
> > Can you send your mkanalysis-sess command? Can you also send one
> > of the
> > regressor files? And can you send the full selxavg3 terminal output?
> >
> > On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> > > I've modified an analysis to include a vector of noise time courses
> > > estimated using ICA. Since IC effects should be consistent across
> > > runs, I'm using taskregs instead of nuisregs. I can define the
> > > analysis and set up contrasts fine; however, when I run the
> analysis
> > > (selxavg3-sess), I get the following error:
> > >
> > > [...]
> > > Saving h.dat to
> > >
> >
>  
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> > > Error using zeros
> > > Size inputs must be integers.
> > >
> > > Error in fast_selxavg3 (line 1248)
> > >   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero
> > for cond 0
> > >
> > > >> --
> > > ERROR: fast_selxavg3() failed\n
> > > a_401_Av_s_task_fmov_bgrnd_icadenoise failed
> > > [...]
> > >
> > > 
> > >
> > > Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than
> > "1" as
> > > usual.
> > >
> > > Any tips on how to debug further?
> > >
> > > _stephen v. shepherd   phd_
> > > The Rockefeller University / 1230 York Avenue / New York NY
> 10065-6307
> > > USA // 212.327.7699 
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
> > 

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[Douglas N Greve]

I don't think it is going to work to have both a -taskreg and a 
paradigm. You should be able to model it as a nuisance regressor. The 
fact that it may be the same across runs won't make much of a difference.
doug

On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote:
> mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm 
> aboutFace.para  -nconditions 13  -TR 2. -rlf 
> rlf_aboutFace_subjvid  -funcstem fm2tas1  -mask brain -analysis 
> a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg 
> taskreg_face__zmove.dat 1  -taskreg taskreg_face__bgrnd.dat 1  
> -taskreg noisereg__TCs_Milo_43.dat 43  -fsd bold -gammafit 0 8  
> -gammaexp 0.3  -polyfit 2  -acfbins 1 -nuisreg motion.dat 3  -force
>
> I've attached example noisereg__TCs_Milo_43.dat and a log which I 
> think includes relevant terminal outputs up to the error. Please let 
> me know if I should provide more information.
>
> s
>
>
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 
> USA // 212.327.7699
>
> On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve 
> > wrote:
>
> Can you send your mkanalysis-sess command? Can you also send one
> of the
> regressor files? And can you send the full selxavg3 terminal output?
>
> On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> > I've modified an analysis to include a vector of noise time courses
> > estimated using ICA. Since IC effects should be consistent across
> > runs, I'm using taskregs instead of nuisregs. I can define the
> > analysis and set up contrasts fine; however, when I run the analysis
> > (selxavg3-sess), I get the following error:
> >
> > [...]
> > Saving h.dat to
> >
> 
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> > Error using zeros
> > Size inputs must be integers.
> >
> > Error in fast_selxavg3 (line 1248)
> >   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero
> for cond 0
> >
> > >> --
> > ERROR: fast_selxavg3() failed\n
> > a_401_Av_s_task_fmov_bgrnd_icadenoise failed
> > [...]
> >
> > 
> >
> > Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than
> "1" as
> > usual.
> >
> > Any tips on how to debug further?
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
> > USA // 212.327.7699 
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

mkanalysis-sess  -native  -event-related  -refeventdur 10  -paradigm
aboutFace.para  -nconditions 13  -TR 2.  -rlf rlf_aboutFace_subjvid
-funcstem fm2tas1  -mask brain  -analysis
a_401_Av_s_task_fmov_bgrnd_icadenoise  -taskreg taskreg_face__zmove.dat 1
-taskreg taskreg_face__bgrnd.dat 1  -taskreg noisereg__TCs_Milo_43.dat 43
-fsd bold  -gammafit 0 8  -gammaexp 0.3  -polyfit 2  -acfbins 1  -nuisreg
motion.dat 3  -force

I've attached example noisereg__TCs_Milo_43.dat and a log which I think
includes relevant terminal outputs up to the error. Please let me know if I
should provide more information.

s



*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699

On Wed, May 4, 2016 at 3:16 PM, Douglas N Greve 
wrote:

> Can you send your mkanalysis-sess command? Can you also send one of the
> regressor files? And can you send the full selxavg3 terminal output?
>
> On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> > I've modified an analysis to include a vector of noise time courses
> > estimated using ICA. Since IC effects should be consistent across
> > runs, I'm using taskregs instead of nuisregs. I can define the
> > analysis and set up contrasts fine; however, when I run the analysis
> > (selxavg3-sess), I get the following error:
> >
> > [...]
> > Saving h.dat to
> >
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> > Error using zeros
> > Size inputs must be integers.
> >
> > Error in fast_selxavg3 (line 1248)
> >   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero for cond 0
> >
> > >> --
> > ERROR: fast_selxavg3() failed\n
> > a_401_Av_s_task_fmov_bgrnd_icadenoise failed
> > [...]
> >
> > 
> >
> > Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than "1" as
> > usual.
> >
> > Any tips on how to debug further?
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
> > USA // 212.327.7699
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you 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.
>
>


noisereg__TCs_Milo_43.dat
Description: Binary data


selxavg3-sess-bold-a_401_Av_s_task_fmov_bgrnd_icadenoise-160504135301 - Copy.log
Description: Binary data
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] External ROI for fcseed

[Douglas N Greve]

You actually need the ROI in the anatomical volume space (ie, the 
"conformed" space of 1mm3, 256^3). If you have a binary (ie, 0,1) mask 
of your ROI called roi.mgz, then use
-seg roi.mgz -segid 1



On 04/28/2016 08:22 PM, Martin Juneja wrote:
> Hi all,
>
> I am trying to perform step-3 from the instructions here:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
> But I do not have segid because the LookUp table FreeSurfer creates 
> after running recon-all doesn't have the area I am interested in. So I 
> defined the ROI externally, converted it into surface using vol2surf 
> and further into .label file using cor2label.
>
> I was wondering how can I use this externally created ROI (either in 
> vol format, or surface format or label format) in this command: 
> fcseed-config.
>
> I made sure that the external ROI is perfectly aligned where it was 
> supposed to be.
>
> Thanks.
> MJ
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Extracting BOLD from a flattened surface

[Douglas N Greve]

Sorry, can you tell me what you are trying to do? You just want a number 
of time points -by- number of vertices file? Then mri_vol2surf should do 
that for you. Flattening is irrelevant for this as it only changes the 
xyz coordinate of the vertex and not the vertex identity.
doug


On 04/29/2016 11:24 AM, Taha Abdullah wrote:
> Hello Freesurfer Experts,
>
> Long story short--I would like to extract BOLD values from each TR 
> across all vertices for one subjects flattened surface
> Following is a brief overview of my steps and at the end you can see 
> where I am stuck.
> First, after */recon-all /I* followed the steps to cut the lh inflated 
> surface, saved as a patch, ran /*mris_flatten, */converted patch into 
> asc file.
> Second, I used read_patch.m to extract all spatial information and a 
> net loss of approximately 10k vertices (127k to 116k)
>
> We had all functional images processed in FSL, the 4D file has 
> 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered 
> the functional and anatomicals together via the following cmd: 
> */ bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold 
> --init-fsl --reg dummy1.da/*t. Afterwards, converted the volume to a 
> surface using the following cmd*/: mri_vol2surf --mov 
> filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp 
> trilinear --hemi lh --o ./lh.func.vol2surf.mgh. /*THe dimensions are 
> 127027 x 1 x 1 x 240. Visually no problem when using*/ tksurfer 
> cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay 
> /lh.func.vol2surf.mgh/  -timecourse lh.func.vol2surf.mgh;/* click on 
> the patch and shows the timecourse for that selected vertex. Using the 
> View>Configure>overlay I can shuffle through the TRs to inspect the 
> change in raw BOLD signal per vertex.
>
> I have been perusing the email web server searching for how to extract 
> the hemodynamic waveform for each vertex across the flattened surface 
> and ultimately will be using matlab to understand how the spatial 
> transformation is happening. As well I have all the matlab files that 
> seemed relevant to my query (read_surf.m, read_patch.m, and 
> readMRI.m). I was hoping that I would be able to have a text file with 
> all the vertices (127K not the flattened 116k) in rows and each column 
> would have the TRs; I ran this command;*/ mri_segstats --slabel 
> cbp001_v1 lh 
> /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label 
> --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh/*, output was the 
> 240 TRs as rows and seems like the average global BOLD signal in the 
> single column corresponding with each TR. Excuse my naiveness, I just 
> recently (1 month ago) started using freesurfer and I feel like I have 
> exhausted as much of the information available on the FS wiki and 
> email server. Any information or advice would be great! I put the 
> commands just to give an idea of my workflow (most of the command 
> lines are from the email server or the FS Wiki) and if there are any 
> issues with my steps please let me know so I can correct them before 
> starting the group analysis.
>
> Best,
> Taha
>
> -- 
> Taha Abdullah
> Department of Physiology
> Northwestern University
> Masters of Science Physiology and Biophysics, Georgetown University 2015
>
>
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Re: [Freesurfer] surface-based spatial smoothing model

[Francesca Strappini]

Thank you!

2016-05-04 21:09 GMT+02:00 Douglas N Greve :

> you can reference this one
> http://www.ncbi.nlm.nih.gov/pubmed/17011792
>
>
>   Smoothing and cluster thresholding for cortical surface-based group
>   analysis of fMRI data.
>
> Hagler DJ Jr
> <
> http://www.ncbi.nlm.nih.gov/pubmed/?term=Hagler%20DJ%20Jr%5BAuthor%5D=true_uid=17011792
> >^1
> , Saygin AP
> <
> http://www.ncbi.nlm.nih.gov/pubmed/?term=Saygin%20AP%5BAuthor%5D=true_uid=17011792
> >,
> Sereno MI
> <
> http://www.ncbi.nlm.nih.gov/pubmed/?term=Sereno%20MI%5BAuthor%5D=true_uid=17011792
> >.
>
>
>
> On 05/03/2016 09:03 AM, Francesca Strappini wrote:
> > Thank you!
> > Is there a paper I can read as a reference?
> >
> > 2016-05-03 15:53 GMT+03:00 Bruce Fischl  > >:
> >
> > Hi Francesca
> >
> > what's the difference? They are both approximations of Gaussians
> > on the
> > surface. We use iterative averaging which is a numerical
> > approximation of
> > a surface-based Gaussian.
> >
> > cheers
> > Bruce
> >
> >
> > On Tue, 3 May 2016, Francesca Strappini wrote:
> >
> > > Hi all,
> > >
> > > I would like to know which model has been implemented for the
> > surface-based
> > > spatial smoothing in Freesurfer (for example in mri_vol2surf).
> > Heat kernel
> > > smoothing and/or diffusion smoothing?
> > >
> > > Thank you
> > > Best
> > >
> > > Francesca
> > >
> > > --
> > > Francesca Strappini, Ph.D.
> > > Neurobiology Department
> > > Weizmann Institute of Science
> > > 234 Herzl Street, Rehovot 7610001 Israel
> > > Tel.: +972 58 444 2584 
> > > E-mail: francesca.strapp...@weizmann.ac.il
> > 
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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.
> >
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il
> > 
> >
> >
> > ___
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> > 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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>
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>



-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] error in fast_selxavg3 (line 1248)

[Douglas N Greve]

Can you send your mkanalysis-sess command? Can you also send one of the 
regressor files? And can you send the full selxavg3 terminal output?

On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote:
> I've modified an analysis to include a vector of noise time courses 
> estimated using ICA. Since IC effects should be consistent across 
> runs, I'm using taskregs instead of nuisregs. I can define the 
> analysis and set up contrasts fine; however, when I run the analysis 
> (selxavg3-sess), I get the following error:
>
> [...]
> Saving h.dat to 
> /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
> Error using zeros
> Size inputs must be integers.
>
> Error in fast_selxavg3 (line 1248)
>   hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero for cond 0
>
> >> --
> ERROR: fast_selxavg3() failed\n
> a_401_Av_s_task_fmov_bgrnd_icadenoise failed
> [...]
>
> 
>
> Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than "1" as 
> usual.
>
> Any tips on how to debug further?
>
> _stephen v. shepherd   phd_
> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 
> USA // 212.327.7699
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Resting-state fcMRI analysis with GLM

[Douglas N Greve]

We don't usually use mri_glmfit for this kind of thing. If you want to 
do it this way, then you cannot use an FSGD file. Instead, create a 
design matrix with the seed time course then pass that to mri_glmfit 
with the --X option (and no --fsgd option).

On 05/04/2016 10:17 AM, Eun Young Choi wrote:
>
> Hi all,
>
> I'd like to run a resting-state fcMRI analysis within the GLM 
> (mri_glmfit), but I'm not completely sure how to set this up in the 
> FSGD file. I've seen the online tutorial of age vs cortical thickness, 
> but I'm not sure how to specify a regressor with a timeseries. Does 
> anyone have an example of an FSGD file for this?
>
> Thanks!
> Eun Young
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] surface-based spatial smoothing model

[Douglas N Greve]

you can reference this one
http://www.ncbi.nlm.nih.gov/pubmed/17011792


  Smoothing and cluster thresholding for cortical surface-based group
  analysis of fMRI data.

Hagler DJ Jr 
^1
 
, Saygin AP 
,
 
Sereno MI 
.



On 05/03/2016 09:03 AM, Francesca Strappini wrote:
> Thank you!
> Is there a paper I can read as a reference?
>
> 2016-05-03 15:53 GMT+03:00 Bruce Fischl  >:
>
> Hi Francesca
>
> what's the difference? They are both approximations of Gaussians
> on the
> surface. We use iterative averaging which is a numerical
> approximation of
> a surface-based Gaussian.
>
> cheers
> Bruce
>
>
> On Tue, 3 May 2016, Francesca Strappini wrote:
>
> > Hi all,
> >
> > I would like to know which model has been implemented for the
> surface-based
> > spatial smoothing in Freesurfer (for example in mri_vol2surf).
> Heat kernel
> > smoothing and/or diffusion smoothing?
> >
> > Thank you
> > Best
> >
> > Francesca
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584 
> > E-mail: francesca.strapp...@weizmann.ac.il
> 
> >
> >
> ___
> 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.
>
>
>
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Symmetric label on fsaverage

[Douglas N Greve]

ive put a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg


On 05/03/2016 04:21 AM, Alexandre Routier wrote:
> Hello Douglas,
>
> Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer 
> 5.3. Is there anything to do to solve this problem ?
>
> Alex
>
> 2016-04-28 18:15 GMT+02:00 Douglas N Greve  >:
>
> You can use mris_left_right_register, then use mris_apply_reg with the
> --src-label option. I can't remember whether these are in 5.3 (or
> whether 5.3 has the --src-label), so let me know if you need updates
>
>
> On 04/28/2016 09:06 AM, Alexandre Routier wrote:
> > Hello everyone,
> >
> > We used tksurfer to draw a specific region on the left hemisphere of
> > fsaverage subject and we would like to automatically register the
> > label from the left hemisphere to the right hemisphere.
> >
> > Since FreeSurfer provides tools to compute a symmetric fsaverage
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was
> wondering if
> > there was any command to have the manually drawn label on the left
> > hemisphere to the right hemisphere.
> >
> > Thanks in advance for your help.
> > Alexandre
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
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> but does not contain patient information, please contact the
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] error in fast_selxavg3 (line 1248)

[S.V.Shepherd [work]]

I've modified an analysis to include a vector of noise time courses
estimated using ICA. Since IC effects should be consistent across runs, I'm
using taskregs instead of nuisregs. I can define the analysis and set up
contrasts fine; however, when I run the analysis (selxavg3-sess), I get the
following error:

[...]
Saving h.dat to
/Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat
Error using zeros
Size inputs must be integers.

Error in fast_selxavg3 (line 1248)
  hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero for cond 0

>> --
ERROR: fast_selxavg3() failed\n
a_401_Av_s_task_fmov_bgrnd_icadenoise failed
[...]



Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than "1" as
usual.

Any tips on how to debug further?

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
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Re: [Freesurfer] no recon button

[Burke,Sarah E]

Douglas, can you please let me know if the voxel edit button is appropriate to 
use in place of the recon edit?

Thanks,

Sarah

Sent from my iPhone

> On May 3, 2016, at 3:04 PM, Burke,Sarah E  wrote:
> 
> 
> Is this information correct?
> 
>> On May 2, 2016, at 3:55 PM, Burke,Sarah E  wrote:
>> 
>> https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Monday, May 2, 2016 3:49 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] no recon button
>> 
>> Can you send us a link to the email you are speaking about?
>> 
>>> On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
>>> It opens a box that says "voxel edit" This allows me to edit the images 
>>> accordingly, however I read in the email forum that this may create some 
>>> issues further on down the line?
>>> 
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: Monday, May 2, 2016 3:26 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] no recon button
>>> 
>>> what happens when you click on the button with the pencil in it? The one
>>> just above the "S" in "Surfaces"
>>> 
 On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
 
 
 
 
 *From:* freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Douglas Greve
 
 *Sent:* Monday, May 2, 2016 2:31 PM
 *To:* freesurfer@nmr.mgh.harvard.edu
 *Subject:* Re: [Freesurfer] no recon button
 Can you send a snapshot of your Freeview window? The Recon Edit button
 looks like a sagittal slice with an "R" in it and a pencil pointing to it.
 
> On 5/2/16 1:44 PM, Burke,Sarah E wrote:
> Thank you Douglas. However, in the tutorial for editing output, it
> says to use the recon edit button to manually perform edits. After
> this step, I use the command line and recon-all. How do I do the
> manual edits without this button. I do see a voxel edit button.
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
> 
> 
> 
> FsTutorial/PialEdits_freeview - Free Surfer Wiki
> 
> surfer.nmr.mgh.harvard.edu
> top | previous Correcting Pial Surfaces. To follow this exercise
> exactly be sure you've downloaded the tutorial data set before you
> begin. If you choose not to ...
> 
> 
> 
> 
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas Greve
> 
> *Sent:* Monday, May 2, 2016 1:29 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] no recon button
> freeview does not have a recon button. You have to run recon-all from
> the command line.
> 
>> On 5/2/16 12:14 PM, Burke,Sarah E wrote:
>> Hello,
>> 
>> 
>> I searched the mail list and saw that others have had this problem,
>> but I see no answers to their queries. I have version 1.0
>> (5/13/2013) of Freeview for Linux.  I have no recon button. What
>> should I do?
>> 
>> 
>> Thank you
>> 
>> 
>> 
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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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
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> 
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[Freesurfer] Resting-state fcMRI analysis with GLM

[Eun Young Choi]

Hi all,

I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit),
but I'm not completely sure how to set this up in the FSGD file. I've seen
the online tutorial of age vs cortical thickness, but I'm not sure how to
specify a regressor with a timeseries. Does anyone have an example of an
FSGD file for this?

Thanks!
Eun Young
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Re: [Freesurfer] downsample fsaverage5 - after and during recon-all

[Bruce Fischl]

Hi Thomas

mri_surf2surf will resample to whatever subject you specific (inludding 
fsaverage5). I'm not sure what using fsaverage5 in recon-all would mean as 
we don't really use fsaverage, but I suspect the answer to your question is 
"no".


cheers
Bruce


On Wed, 4 May 2016, Wolfers, T. (Thomas) wrote:


Is there an easy option to re-sample surface (area.pial and thickness) into
fsaverage5 space?
How is it possible to use fsaverage5 instead of fsaverage for recon-all?

Many thanks for your answers

Thomas Wolfers
Donders Center for Cognitive Neuroimaging
Kapittelweg 29
6525EN Nijmegen
The Netherlands

Tel:  0031/2436/10098

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Re: [Freesurfer] Correcting defect

[Bruce Fischl]

sure. Or you can load the ?h.inflated.nofix and look at it - it should be 
obvious if there is a huge defect (you can also load the file 
?h.defect_labels as an overlay on that surface and it will show you the 
segmentation of the defects)


cheers
Bruce
On Wed, 4 May 2016, Katarina Trojacanec wrote:



Dear FreeSurfer Team,


I have been trying to run creation of template with FreeSurfer. However,
for two cases for one patient (case 1: template based on TP1 and TP4, case
2: template based on TP2 and TP4), the correcting defect step is running
too long. According to the information in the mail archive, the defects are
probably too big, and that is the reason for the long processing. 


May I send you via ftp the subjects directories so you can help me to
proceed with this subject, because I am not able to figure out and correct
the problem? Should I send you the base directories in their current state
or the cross-sectionally processed time points as well?


Best Regards, 


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia  

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[Freesurfer] downsample fsaverage5 - after and during recon-all

[Wolfers, T. (Thomas)]

Is there an easy option to re-sample surface (area.pial and thickness) into 
fsaverage5 space?
How is it possible to use fsaverage5 instead of fsaverage for recon-all?

Many thanks for your answers

Thomas Wolfers
Donders Center for Cognitive Neuroimaging
Kapittelweg 29
6525EN Nijmegen
The Netherlands

Tel:  0031/2436/10098
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Re: [Freesurfer] Brainstem segmentation

[Eugenio Iglesias]

Dear Haque, 
FreeSurfer 6 has not been released yet. But if you want to try the brainstem 
segmentation module, you can download the dev version; you will find it in 
there. 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Haque, Muhammad E"  
To: "Freesurfer support list"  
Sent: Monday, May 2, 2016 5:24:48 PM 
Subject: [Freesurfer] Brainstem segmentation 



Dear FreeSurfer Users, 



I would like to know if we can do brainstem segmentation as described in the 
recent publication 

http://www.sciencedirect.com/science/article/pii/S1053811915001895 




Author as well as FreeSurfer website mention that this feature is only 
available in FreeSurfer 6.0 and later version 



https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures 




Where I can download this FreeSurfer 6.0? 



Thanks. 



Haque 

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properly 
dispose of the e-mail. 
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[Freesurfer] Correcting defect

[Katarina Trojacanec]

Dear FreeSurfer Team,


I have been trying to run creation of template with FreeSurfer. However, for 
two cases for one patient (case 1: template based on TP1 and TP4, case 2: 
template based on TP2 and TP4), the correcting defect step is running too long. 
According to the information in the mail archive, the defects are probably too 
big, and that is the reason for the long processing.


May I send you via ftp the subjects directories so you can help me to proceed 
with this subject, because I am not able to figure out and correct the problem? 
Should I send you the base directories in their current state or the 
cross-sectionally processed time points as well?


Best Regards,


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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