[Freesurfer] Retinotopy stimuli

[Anders Hougaard]

Dear freesurfers,


Which stimuli do you think provide the best retinotopic maps?

I have done a retinotopy analysis using the following stimuli:

Polar angle:

- 45 deg counter-clockwise rotating wedge
- 8 unique positions
- flickering at 2 Hz
- stimulation period: 36 sec
- no. of cycles: 6
- TR = 3

Eccentricity:

 - expanding ring
- 8 unique positions
- flickering at 2 Hz
- stimulation period: 36 sec
- no. of cycles: 6
- TR = 3

Any suggestions on how to optimize this stimulation?
E.g. different period length, more runs, bi-directional, different TR

Thank you!

Best regards,

Anders
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Re: [Freesurfer] Error while loading qdec project file

[Tetiana Dadakova]

Hi Nick,

I have Mac OS X 10.6.7.
Now I found the tmp folder, and can explain in more details what happens:
As I save the Project File, the qdec_project_archive/qdec.table.dat is
created, but it exists in /tmp only for several seconds and then
disappears.
Have you heard about something like this before? Do you know what the
problem can be?

Thank you,
Tanja.


On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky
 wrote:
> what is your operating system?  linux and mac typically have a /tmp dir,
> unless you're running on a cluster?
>
> n.
>
> On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote:
>> Dear experts,
>>
>> When I try to load a saved Project File, I get an error:
>>
>> Loading data table /tmp/qdec_project_archive/qdec.table.dat...
>> ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
>> Error loading the project file.
>>
>> I do not have any /tmp subdirectory. Should it appear when I save the
>> Project File? Should it be in /qdec directory?
>>
>> Thank you,
>> Tanja.
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Re: [Freesurfer] tracula bvecs problem

[Franz Liem]

Dear Anastasia & all.

I fixed it.

The problem was my LOCALE setting which leads to different handling of decimal 
separators by awk (for further details see 
http://objectmix.com/awk/716715-awk-different-decimal-separator-different-linux-distros.html).

My original setting was:
% locale
LANG="de_CH.UTF-8"
LC_COLLATE="de_CH.UTF-8"
LC_CTYPE="de_CH.UTF-8"
LC_MESSAGES="de_CH.UTF-8"
LC_MONETARY="de_CH.UTF-8"
LC_NUMERIC="de_CH.UTF-8"
LC_TIME="de_CH.UTF-8"
LC_ALL=

Therefore awk used the comma as decimal separator.

In order to change this I added the following line to the .tcshrc file:
setenv LC_ALL en_US

resulting in:
% locale
LANG="de_CH.UTF-8"
LC_COLLATE="en_US"
LC_CTYPE="en_US"
LC_MESSAGES="en_US"
LC_MONETARY="en_US"
LC_NUMERIC="en_US"
LC_TIME="en_US"
LC_ALL="en_US"

Now the bvec rotation and correction works fine.

Is your setting en_US or another format (e.g. en_US.ISO8859-1, 
en_US.ISO8859-15, en_US.US-ASCII, en_US.UTF-8)?


Anastasia and Priti, thank you for your time.

Best,
Franz 

Am 06.07.2011 um 21:32 schrieb Anastasia Yendiki:

> 
> I'm attaching what I get when I run it. Only the trailing zeros are missing.
> 
> On Wed, 6 Jul 2011, Franz Liem wrote:
> 
>> If i flip4fsl my fake file the the numbers after the decimal point are 
>> missing in the output (bvecs_bvecs_onezero3decpoint1_western_out).
>> 
>> I have attached a fake bvecs fitting your tutorial data (70 lines). Would 
>> you be so kind, as to run this.
>> 
>> Thank you so much for your help,
>> Franz
>> 
>> 
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[Freesurfer] bbregister - Are 6 dof enough for MNI305?

[Joao Pereira]

Dear Freesurfers,

I was wondering if you could help me clarify one question I have re
 the recommended use of bbregister to register PET data.

If I want to register my PET data to MNI305 space used in Freesurfer,
 is a 6 dof rigid registration enough? 
I notice that the tailarach function used within autorecon1 is a 12
 dof affine, so I'm guessing that bbregister is unlikely to fully
 register the PET data to the template space in the same way that (eg)
 brain.mgz is registered.

Thank you very much!

Best,

Joao Pereira


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Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?

[Bruce Fischl]

Hi Joao

You are registering to that subject's anatomicals, not a template, so 6 should 
be enough
Cheers
Bruce
On Jul 7, 2011, at 6:43 AM, Joao Pereira  wrote:

> Joao
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[Freesurfer] QDEC table

[Ignacio Letelier]

Hi freesurfers

Do anyone know if it's possible to automatically enter in the QDEC table the
gray matter volume  of every subject in the study, to avoid
entering this item manually for each one ?

Best regards.
-- 
Ignacio.
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[Freesurfer] freeview load fiducials from 3DSlicer

[Gabriele Arnulfo]

Hi guys,

I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to
import them within freeview? Those points look like 

label,x,y,z,[flag],[flag]
i.e.
P,57.799,-49.1799,13.07,1,1
P,-4.05607,-47.1519,8.93645,1,1

thank in advance.


g.


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Re: [Freesurfer] Matlab and FS

[Carolina Valencia]

Hi Jorge,
Thanks for your reply,  I installed Octave in the Ubuntu machine, Should I
setup something in order to use the FS commands?
Best regards,
Carolina

2011/7/5 jorge luis 

>
>
> Hi Carolina
>
>  **
>
> There is a directory freesurfer/matlab which contains several matlab-based
> scripts for reading and writing (after modified) surface- and volume-based
> data generated in freesurfer. 
>
> Transport files from Linux to Windows will be tedious and things may not
> work properly, therefore, I recommend you to install Matlab for Linux or you
> can try with Octave (a kind of GNU Matlab for Linux).
>
> ** **
>
> Cheers 
>
> Jorge
>
> --- El *mar, 5/7/11, Carolina Valencia *escribió:
>
>
> De: Carolina Valencia 
> Asunto: [Freesurfer] Matlab and FS
> Para: freesurfer@nmr.mgh.harvard.edu
> Fecha: martes, 5 de julio, 2011 17:39
>
>
> Hello FS'users,
>
> I'm trying to do an histogram of cortical thickness for 2 cases in matlab,
> but the problem is that I have Installed matlab in a computer (windows) and
> FS in another one (ubuntu)
> Can I configure something to use the FS commands in matlab in order to
> obtain some graphs?
> And also, where can I find the cortical thickness in each regions (Brodmann
> areas, gyrus or sulci) of the brain in order to compare a normal patient
> with a patiwnt who has a cortical dysplasia ?
>
> Thanks a lot for your help,
>
> Carolina
>
>
> -Adjunto en línea a continuación-
>
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-- 
-- 
*Carolina Valencia Muñoz*
Bioingeniera
*LINK DIAGNOSTICO DIGITAL SA
*Cel: 3016411824
Of: (4) 444 54 65
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[Freesurfer] cortical dysplasia

[Carolina Valencia]

Hello FSexperts

I have a MPRAGE image of cortical dysplasia, I have some regions of
grey matter within the white matter, and I measured the cortical
thickness in the projections of those regions and I expected to find a
thinnercortex instead I found a cortical thickening. FS takes into
account the embedded region of the grey matter to measure the cortical
thickness?

Best regards,

Carolina
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Re: [Freesurfer] cortical dysplasia

[Pedro Paulo de Magalhães Oliveira Junior]

Carolina,

We have worked with several cases of MCD (including cortical dysplasia). We
have published this paper:
https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf

It may help.

But in most cases of cortical dysplasia (not Gray matter heterotopia cases)
you'll find a ticker cortex not a thinner one. But maybe you could post one
image illustrate this problem.

PPJ




On Thu, Jul 7, 2011 at 10:39, Carolina Valencia wrote:

> Hello FSexperts
>
> I have a MPRAGE image of cortical dysplasia, I have some regions of grey 
> matter within the white matter, and I measured the cortical thickness in the 
> projections of those regions and I expected to find a thinnercortex instead I 
> found a cortical thickening. FS takes into account the embedded region of the 
> grey matter to measure the cortical thickness?
>
> Best regards,
>
> Carolina
>
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Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?

[Douglas N Greve]

The conversion from PET to MNI305 uses two registration steps. One from 
PET to anatomical, one from anat to mni305. bbregister handles the first 
one, so 6 dof is fine.
doug

Joao Pereira wrote:
> Dear Freesurfers,
>
> I was wondering if you could help me clarify one question I have re
>  the recommended use of bbregister to register PET data.
>
> If I want to register my PET data to MNI305 space used in Freesurfer,
>  is a 6 dof rigid registration enough? 
> I notice that the tailarach function used within autorecon1 is a 12
>  dof affine, so I'm guessing that bbregister is unlikely to fully
>  register the PET data to the template space in the same way that (eg)
>  brain.mgz is registered.
>
> Thank you very much!
>
> Best,
>
> Joao Pereira
>
>
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>   

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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] matlab loading problem (mkcontrast, selxavg3-sess)

[Douglas N Greve]

Hi Paola, I can't tell from the output what went wrong. One thing that 
may be going wrong is that you might not have the matlab binary in your 
path. From a terminal, type 'which matlab' (no quotes). Also, please 
don't send logs and error messages in rtf or doc formats -- it makes it 
harder for us to read!
thanks

doug

Paola Binda wrote:
>
> Hi all
> I'm having trouble with the interface between freesurfer and matlab too
> in my case, running mkcontrast does not open matlab and eventually 
> generates an error
>
> Any help to work around this problem would be very much appreciated
>
> I'm running freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on a Mac 
> OS X 10.6.8 (please see details of the system/command/error message in 
> the rtf file in attach)
> I've just installed Freesurfer and this is the first time I try this 
> command
>
>
> Paola
>
> 
>
>
>
>>
>>
>> What is your platform and what version of FS are you using?
>>
>> doug
>>
>> On 12/15/10 2:42 PM, Katherine Sledge Moore wrote:
>> > I am having trouble with the interface between freesurfer and 
>> matlab. When I 
>> > run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing 
>> happens (the 
>> > script does not finish.) When I force it to quit, I get the error 
>> "-display: 
>> > Command not found." In both mkcontrast and selxavg3-sess, the 
>> command to call 
>> > matlab is something along the lines of "matlab -display iconic". 
>> Any thoughts 
>> > as to why the "-display iconic" part is not being interpreted?
>> >
>> > Katherine Sledge Moore
>> > Postdoctoral Associate
>> > Visual Cognitive Neuroscience Laboratory
>> > Yale University
>> > 
>> http://camplab.psych.yale.edu/
>>
>> > 
>> http://pantheon.yale.edu/~khs8 
>>
>> >
>> >
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>> >
>> >
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[Freesurfer] Viewing a multi-frame image?

[Agnieszka Burzynska]

Dear all,
I created a 3-frame image using a command similar to:
mris_preproc --target fsaverage --hemi lh --fwhm 5 \
  --out xrun/lh.cope1.mgh \
  --iv fbert1.feat/stats/cope1.nii.gz
fbert1.feat/reg/freesurfer/anat2exf.register.dat \
  --iv fbert2.feat/stats/cope1.nii.gz
fbert2.feat/reg/freesurfer/anat2exf.register.dat


How can I view all 3 frames of the lh.cope1.mgh?
I see just one frame with:
tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh
And don't know how to toggle between the frames.

Thank you for your help!

Cheers,
Aga



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Re: [Freesurfer] Viewing a multi-frame image?

[Douglas N Greve]

Hi Aga, try View->Configure->Overlay. The config window will have a time 
point entry at the top.
doug

Agnieszka Burzynska wrote:
> Dear all,
> I created a 3-frame image using a command similar to:
> mris_preproc --target fsaverage --hemi lh --fwhm 5 \
>   --out xrun/lh.cope1.mgh \
>   --iv fbert1.feat/stats/cope1.nii.gz
> fbert1.feat/reg/freesurfer/anat2exf.register.dat \
>   --iv fbert2.feat/stats/cope1.nii.gz
> fbert2.feat/reg/freesurfer/anat2exf.register.dat
>
>
> How can I view all 3 frames of the lh.cope1.mgh?
> I see just one frame with:
> tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh
> And don't know how to toggle between the frames.
>
> Thank you for your help!
>
> Cheers,
> Aga
>
>
>
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[Freesurfer] make_average_subject error

[leonardo kay]

Hi all

Could anyone help me with this error:

MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
annot file:
/home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot


This appeared after trying to average my subject data. It says ' vertex
index out of range '. All acquisitions were made
using the same parameters so I don't know what this may mean.


Thanks in advance

-- 
Leo Kay.
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Re: [Freesurfer] Viewing a multi-frame image?

[Agnieszka Burzynska]

Dear Doug,
Yes, it works, thank you so much!
Cheers,
Aga

On 7/7/11 3:57 PM, "Douglas N Greve"  wrote:

> Hi Aga, try View->Configure->Overlay. The config window will have a time
> point entry at the top.
> doug
> 
> Agnieszka Burzynska wrote:
>> Dear all,
>> I created a 3-frame image using a command similar to:
>> mris_preproc --target fsaverage --hemi lh --fwhm 5 \
>>   --out xrun/lh.cope1.mgh \
>>   --iv fbert1.feat/stats/cope1.nii.gz
>> fbert1.feat/reg/freesurfer/anat2exf.register.dat \
>>   --iv fbert2.feat/stats/cope1.nii.gz
>> fbert2.feat/reg/freesurfer/anat2exf.register.dat
>> 
>> 
>> How can I view all 3 frames of the lh.cope1.mgh?
>> I see just one frame with:
>> tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh
>> And don't know how to toggle between the frames.
>> 
>> Thank you for your help!
>> 
>> Cheers,
>> Aga
>> 
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>>   

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Re: [Freesurfer] make_average_subject error

[Douglas N Greve]

Hi Leo, check to see if that subject's analysis is up-to-date. This 
usually happens when it was only partially re-run.
doug

leonardo kay wrote:
> Hi all
>
> Could anyone help me with this error:
>
> MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 
> i=5A595959, in_array_size=133467
> annot file: 
> /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot
>
>
> This appeared after trying to average my subject data. It says ' 
> vertex index out of range '. All acquisitions were made
> using the same parameters so I don't know what this may mean.
>
>
> Thanks in advance
>  
> -- 
> Leo Kay.
>
> 
>
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Fax: 617-726-7422

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Re: [Freesurfer] more on fieldsign problems-

[Douglas N Greve]

Hi Michelle, do the eccen and polar maps look ok? Also, I would probably 
smooth them a little bit. The field sign calculation is basically a 
spatial derivative so it can be sensitive to noise.
doug

Michelle Umali wrote:
> Dear all,
>   I've been having issues with my fieldsign images all I get are  
> speckles. I did the following and did not get any errors:
>
> 1) ran recon-all -all
> 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
> 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat
> 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48  
> paradigm
> rtopy.par -nskip 4 fwhm 0
> 5) selxavg3-sess -a rtopy.self.rh -s sj09
> 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
>
> When I looked at the fieldsign map using:
> 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
>
> all I got were blue and red speckles.  The polar and eccentricity maps  
> seemed ok.
>
>
> Any help would be great.
>
> Michelle
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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

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Re: [Freesurfer] QDEC table

[Nick Schmansky]

the 'generate stats data tables' button in the Subjects tab will do
this.  see the section 'Stats Data Import' in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
which is copied here:


> It is possible to import the aseg and aparc data from the
> FreeSurfer-processed group data. To do so, press the 'Generate Stats
> Data Tables' button. This will run the FreeSurfer utilities
> asegstats2table and aparcstats2table on your group data. Upon
> completion (you should see the progress in the terminal screen), then
> the 'Generate Stats Data Tables' button becomes a menu-selection list.
> Within that menu, you can select 'aseg.volume'. Upon doing so, the
> volumetric data for various subcortical structures are displayed. You
> could choose for example 'Left-Lateral-Ventricle', then click 'Add
> Selection to Data Table'. Upon doing so, it will appear in the
> 'Discrete and Continuous Factors' display of the 'Data Table View'.
> 'Left-Lateral-Ventricle' is now available as a possible factor in your
> analysis ('Left-Hippocampus' and 'Right-Hippocampus' were imported
> from aseg.volume in this manner). If you select
> 'Left-Lateral-Ventricle' in the 'Data Table View', then the volumetric
> data for all the subjects is plotted. You can look for patterns or
> outliers. If you suspect an outlier, right-click on that point in the
> scatter-plot. You can then either exclude that subject, or examine it
> in tkmedit or tksurfer, to check for possible problems in the original
> scan data. Lastly, you can save this newly imported data (in this
> case, 'Left-Lateral-Ventricle') to your qdec.table.dat file by
> selecting 'Save Data Table' from the File menu (but dont do this for
> the tutorial). 
> 


n.



On Thu, 2011-07-07 at 09:18 -0400, Ignacio Letelier wrote:
> Hi freesurfers
> 
> Do anyone know if it's possible to automatically enter in the QDEC
> table the gray matter volume  of every subject in the study, to avoid 
> entering this item manually for each one ?
> 
> Best regards.
> -- 
> Ignacio.
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[Freesurfer] DOF and smoothing in mri_glmfit

[Agnieszka Burzynska]

Dear all,
I am combining 3 runs of a subject using fixed effects GLM and I wanted to
make sure I am doing the right thing.

For each subject I use:
mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
$SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5

, while lh.cope1.mgh contains the concatenated cope1 images of the same
subject in fsaverage space (the same for varcope1).

1) Is it the right way?
2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it
correct?
3) The functional data has not been smoothed in the 1st level analysis in
FSL (as recommended), and also not smoothed during sampling the copes to a
common space. Therefore I want to smooth it here for the first time, but
only with 5mm. Does it sound right?

Cheers,
Aga

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Re: [Freesurfer] DOF and smoothing in mri_glmfit

[Douglas N Greve]

Hi Aga, your commands look right. For the DOF, it should be the sum of 
the DOFs from all the runs (probably won't make much of a difference). 
Smoothing is a bit of an issue when you want to look at individual 
results. Technically, you should smooth before you do the first level 
analysis (ie, before your compute the varcope), but this would require 
doing the FEAT analysis directly on surface data. Smoothing after 
computing the varcope means that the varcope will not be accurate (it 
will be too large). The penalty is that you will see less activation 
than you should. At the group level, this is not such a big deal because 
you're either not using the varcope or you are using it as a weight.
doug

Agnieszka Burzynska wrote:
> Dear all,
> I am combining 3 runs of a subject using fixed effects GLM and I wanted to
> make sure I am doing the right thing.
>
> For each subject I use:
> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5
>
> , while lh.cope1.mgh contains the concatenated cope1 images of the same
> subject in fsaverage space (the same for varcope1).
>
> 1) Is it the right way?
> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it
> correct?
> 3) The functional data has not been smoothed in the 1st level analysis in
> FSL (as recommended), and also not smoothed during sampling the copes to a
> common space. Therefore I want to smooth it here for the first time, but
> only with 5mm. Does it sound right?
>
> Cheers,
> Aga
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

-- 
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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] DOF and smoothing in mri_glmfit

[Agnieszka Burzynska]

Dear Doug,
Thank you so much. I completely see you point, but I have re-run the 1st
level feat without smoothing just because it has been recommended not to
smooth in the volume and then transfer it onto the surface, but rather first
smooth on the surface
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer).

What I plan to do in the end is to include the cortical thickness as the
vertex-wise covariate in the functional group analysis.

So the final analysis will be on the group level, where, as you say, the
varcopes should not matter that much.

However, I was also thinking of analyzing varcopes in addition to copes
(group analysis) to relate the variance of BOLD signal to the thickness.

Would you then recommend going back and taking the initial 1st level
analysis with regular smoothing?

Thank you!
Aga

On 7/7/11 4:43 PM, "Douglas N Greve"  wrote:

> Hi Aga, your commands look right. For the DOF, it should be the sum of
> the DOFs from all the runs (probably won't make much of a difference).
> Smoothing is a bit of an issue when you want to look at individual
> results. Technically, you should smooth before you do the first level
> analysis (ie, before your compute the varcope), but this would require
> doing the FEAT analysis directly on surface data. Smoothing after
> computing the varcope means that the varcope will not be accurate (it
> will be too large). The penalty is that you will see less activation
> than you should. At the group level, this is not such a big deal because
> you're either not using the varcope or you are using it as a weight.
> doug
> 
> Agnieszka Burzynska wrote:
>> Dear all,
>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to
>> make sure I am doing the right thing.
>> 
>> For each subject I use:
>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5
>> 
>> , while lh.cope1.mgh contains the concatenated cope1 images of the same
>> subject in fsaverage space (the same for varcope1).
>> 
>> 1) Is it the right way?
>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it
>> correct?
>> 3) The functional data has not been smoothed in the 1st level analysis in
>> FSL (as recommended), and also not smoothed during sampling the copes to a
>> common space. Therefore I want to smooth it here for the first time, but
>> only with 5mm. Does it sound right?
>> 
>> Cheers,
>> Aga
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>>   

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Re: [Freesurfer] Retinotopy stimuli

[Thomas Ballinger]

I'd also be very interested to hear about good reinotopic stimuli; we've
used 6Hz and 14 ring sizes for eccentricity mapping in the past.

Thomas Ballinger

On Thu, Jul 7, 2011 at 3:56 AM, Anders Hougaard wrote:

> Dear freesurfers,
>
>
> Which stimuli do you think provide the best retinotopic maps?
>
> I have done a retinotopy analysis using the following stimuli:
>
> Polar angle:
>
> - 45 deg counter-clockwise rotating wedge
> - 8 unique positions
> - flickering at 2 Hz
> - stimulation period: 36 sec
> - no. of cycles: 6
> - TR = 3
>
> Eccentricity:
>
>  - expanding ring
> - 8 unique positions
> - flickering at 2 Hz
> - stimulation period: 36 sec
> - no. of cycles: 6
> - TR = 3
>
> Any suggestions on how to optimize this stimulation?
> E.g. different period length, more runs, bi-directional, different TR
>
> Thank you!
>
> Best regards,
>
> Anders
>
>
>
>
>
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>
>
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Re: [Freesurfer] DOF and smoothing in mri_glmfit

[Douglas N Greve]

The problem with doing the smoothing at the first level in FEAT is that 
it will be volume-based, not surface-based. I'm not sure what to tell 
you about using the varcopes. They will certainly be very noisy without 
smoothing, so probably smoothing is a good idea, even if it's volume-based.

doug

Agnieszka Burzynska wrote:
> Dear Doug,
> Thank you so much. I completely see you point, but I have re-run the 1st
> level feat without smoothing just because it has been recommended not to
> smooth in the volume and then transfer it onto the surface, but rather first
> smooth on the surface
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer).
>
> What I plan to do in the end is to include the cortical thickness as the
> vertex-wise covariate in the functional group analysis.
>
> So the final analysis will be on the group level, where, as you say, the
> varcopes should not matter that much.
>
> However, I was also thinking of analyzing varcopes in addition to copes
> (group analysis) to relate the variance of BOLD signal to the thickness.
>
> Would you then recommend going back and taking the initial 1st level
> analysis with regular smoothing?
>
> Thank you!
> Aga
>
> On 7/7/11 4:43 PM, "Douglas N Greve"  wrote:
>
>   
>> Hi Aga, your commands look right. For the DOF, it should be the sum of
>> the DOFs from all the runs (probably won't make much of a difference).
>> Smoothing is a bit of an issue when you want to look at individual
>> results. Technically, you should smooth before you do the first level
>> analysis (ie, before your compute the varcope), but this would require
>> doing the FEAT analysis directly on surface data. Smoothing after
>> computing the varcope means that the varcope will not be accurate (it
>> will be too large). The penalty is that you will see less activation
>> than you should. At the group level, this is not such a big deal because
>> you're either not using the varcope or you are using it as a weight.
>> doug
>>
>> Agnieszka Burzynska wrote:
>> 
>>> Dear all,
>>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to
>>> make sure I am doing the right thing.
>>>
>>> For each subject I use:
>>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
>>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
>>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5
>>>
>>> , while lh.cope1.mgh contains the concatenated cope1 images of the same
>>> subject in fsaverage space (the same for varcope1).
>>>
>>> 1) Is it the right way?
>>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it
>>> correct?
>>> 3) The functional data has not been smoothed in the 1st level analysis in
>>> FSL (as recommended), and also not smoothed during sampling the copes to a
>>> common space. Therefore I want to smooth it here for the first time, but
>>> only with 5mm. Does it sound right?
>>>
>>> Cheers,
>>> Aga
>>>
>>> ___
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] tracula bvecs problem

[Anastasia Yendiki]

Great, good to know. My LANG is en_US.UTF-8, everything else is not set.

On Thu, 7 Jul 2011, Franz Liem wrote:

> Dear Anastasia & all.
>
> I fixed it.
>
> The problem was my LOCALE setting which leads to different handling of 
> decimal separators by awk (for further details see 
> http://objectmix.com/awk/716715-awk-different-decimal-separator-different-linux-distros.html).
>
> My original setting was:
> % locale
> LANG="de_CH.UTF-8"
> LC_COLLATE="de_CH.UTF-8"
> LC_CTYPE="de_CH.UTF-8"
> LC_MESSAGES="de_CH.UTF-8"
> LC_MONETARY="de_CH.UTF-8"
> LC_NUMERIC="de_CH.UTF-8"
> LC_TIME="de_CH.UTF-8"
> LC_ALL=
>
> Therefore awk used the comma as decimal separator.
>
> In order to change this I added the following line to the .tcshrc file:
> setenv LC_ALL en_US
>
> resulting in:
> % locale
> LANG="de_CH.UTF-8"
> LC_COLLATE="en_US"
> LC_CTYPE="en_US"
> LC_MESSAGES="en_US"
> LC_MONETARY="en_US"
> LC_NUMERIC="en_US"
> LC_TIME="en_US"
> LC_ALL="en_US"
>
> Now the bvec rotation and correction works fine.
>
> Is your setting en_US or another format (e.g. en_US.ISO8859-1, 
> en_US.ISO8859-15, en_US.US-ASCII, en_US.UTF-8)?
>
>
> Anastasia and Priti, thank you for your time.
>
> Best,
> Franz
>
> Am 06.07.2011 um 21:32 schrieb Anastasia Yendiki:
>
>>
>> I'm attaching what I get when I run it. Only the trailing zeros are missing.
>>
>> On Wed, 6 Jul 2011, Franz Liem wrote:
>>
>>> If i flip4fsl my fake file the the numbers after the decimal point are 
>>> missing in the output (bvecs_bvecs_onezero3decpoint1_western_out).
>>>
>>> I have attached a fake bvecs fitting your tutorial data (70 lines). Would 
>>> you be so kind, as to run this.
>>>
>>> Thank you so much for your help,
>>> Franz
>>>
>>>
>> ___
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>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] Retinotopy stimuli

[Jonathan Polimeni]

hi anders,

the optimal set of stimulus parameters will depend somewhat on what
cortical area(s) you are trying to map and on the details of your
acquisition. in general, stimulating with both clockwise- and
counterclockwise-rotating wedges for polar angle mapping and with both
expanding and contracting rings for eccentricity mapping improves the
accuracy of the maps, and the proper analysis of this data is implemented
fsfast. the width of the wedge or the ring will depend on the cortical
area you are trying to stimulate, but you may want to consider a thinner
wedge. also, 8 Hz flickering has been shown to activate area V1 more
strongly than other frequencies, and smoothly moving stimuli can also
help. then, depending on your voxel size, field strength, coil array,
etc., you could include more cycles and may need to average together
multiple runs.

marty, roger et al. have a few nice papers that i'd recommend that discuss
some of these details relating to phase-encoded retinotopic stimuli.

  Sereno & Tootell. Curr Opin Neurobiol. 2005;15(2):135-44.
  Tootell et al. J Neurosci. 1997;17(18):7060-78.
  Sereno et al. Science. 1995;268(5212):889-93.

(the '97 paper discusses the ring/wedge thickness, the '95 paper discusses
the advantages of using both expanding + contracting stimuli, and the '05
paper discusses the use of smoothly varying stimuli.)

hope this helps. were you able to get reasonable looking maps with the
stimuli you described below?


-jon




On Thu, 7 Jul 2011, Anders Hougaard wrote:

> Dear freesurfers,
>
>
> Which stimuli do you think provide the best retinotopic maps?
>
> I have done a retinotopy analysis using the following stimuli:
>
> Polar angle:
>
> - 45 deg counter-clockwise rotating wedge
> - 8 unique positions
> - flickering at 2 Hz
> - stimulation period: 36 sec
> - no. of cycles: 6
> - TR = 3
>
> Eccentricity:
>
>  - expanding ring
> - 8 unique positions
> - flickering at 2 Hz
> - stimulation period: 36 sec
> - no. of cycles: 6
> - TR = 3
>
> Any suggestions on how to optimize this stimulation?
> E.g. different period length, more runs, bi-directional, different TR
>
> Thank you!
>
> Best regards,
>
> Anders
>
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Re: [Freesurfer] Retinotopy stimuli

[Don Hagler]

Hi Anders,

I agree with the points Jon made.  8 Hz flicker is also what I use.  I haven't 
tried lower frequencies, but
 I think you would definitely have reduced SNR if you did.  I also use rather 
thin wedges and rings and smoothly vary their position.


I would add that a longer cycle duration (e.g. 64 seconds) seems to provide 
better phase estimates.  I had been using a shorter duration (32 seconds) for 
awhile, and while you can get reasonable results (and better SNR because of 
more cycles/scan), I was also noticing irregularities in the maps (e.g. spots 
of upper field preference where it should be lower field).  When I did a direct 
comparison between the two cycle durations, the maps looked much cleaner with 
the longer cycle.

Because the data can be rather noisy (regardless of field strength), multiple 
scans are important.  I use 4 scans for polar angle (2 CW, 2 CCW) and 2 for 
eccentricity (1 expanding, 1 contracting), although I would do more in a 
session if I thought the typical subject could stand it.  My current settings 
are 5 cycles/scan, 64 second cycle duration, 128 TRs, TR = 2.5 sec, so ~5.5 
minutes / scan.  A 3 sec TR would work fine too, and allow for 6 cycles/scan, 
which would improve SNR (and increase total scan duration).

Don

> Date: Thu, 7 Jul 2011 11:30:13 -0400
> From: j...@nmr.mgh.harvard.edu
> To: ahouga...@dadlnet.dk
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Retinotopy stimuli
> 
> 
> hi anders,
> 
> the optimal set of stimulus parameters will depend somewhat on what
> cortical area(s) you are trying to map and on the details of your
> acquisition. in general, stimulating with both clockwise- and
> counterclockwise-rotating wedges for polar angle mapping and with both
> expanding and contracting rings for eccentricity mapping improves the
> accuracy of the maps, and the proper analysis of this data is implemented
> fsfast. the width of the wedge or the ring will depend on the cortical
> area you are trying to stimulate, but you may want to consider a thinner
> wedge. also, 8 Hz flickering has been shown to activate area V1 more
> strongly than other frequencies, and smoothly moving stimuli can also
> help. then, depending on your voxel size, field strength, coil array,
> etc., you could include more cycles and may need to average together
> multiple runs.
> 
> marty, roger et al. have a few nice papers that i'd recommend that discuss
> some of these details relating to phase-encoded retinotopic stimuli.
> 
>   Sereno & Tootell. Curr Opin Neurobiol. 2005;15(2):135-44.
>   Tootell et al. J Neurosci. 1997;17(18):7060-78.
>   Sereno et al. Science. 1995;268(5212):889-93.
> 
> (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses
> the advantages of using both expanding + contracting stimuli, and the '05
> paper discusses the use of smoothly varying stimuli.)
> 
> hope this helps. were you able to get reasonable looking maps with the
> stimuli you described below?
> 
> 
> -jon
> 
> 
> 
> 
> On Thu, 7 Jul 2011, Anders Hougaard wrote:
> 
> > Dear freesurfers,
> >
> >
> > Which stimuli do you think provide the best retinotopic maps?
> >
> > I have done a retinotopy analysis using the following stimuli:
> >
> > Polar angle:
> >
> > - 45 deg counter-clockwise rotating wedge
> > - 8 unique positions
> > - flickering at 2 Hz
> > - stimulation period: 36 sec
> > - no. of cycles: 6
> > - TR = 3
> >
> > Eccentricity:
> >
> >  - expanding ring
> > - 8 unique positions
> > - flickering at 2 Hz
> > - stimulation period: 36 sec
> > - no. of cycles: 6
> > - TR = 3
> >
> > Any suggestions on how to optimize this stimulation?
> > E.g. different period length, more runs, bi-directional, different TR
> >
> > Thank you!
> >
> > Best regards,
> >
> > Anders
> >
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
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> at
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> properly
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[Freesurfer] talaraich ERROR

[Carolina Valencia]

Hi FSexperts,

I have a case of a child with *Hydrocephalus and cortical dysplasia, the
patient has a subcutaneous ventriculo-peritoneal shunt that produces an
artifice in all MRI sequences, I try to recon-all but it exit with ERROR*
#
#@# Talairach Failure Detection Thu Jul  7 11:03:21 COT 2011
/home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)
Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #54-Ubuntu
SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux

recon-all -s hptu_vol04 exited with ERRORS at Thu Jul  7 11:03:21 COT 2011

is possible to process it in automated fashion?

Thanks,

Best regards,

Carolina
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Re: [Freesurfer] Matlab and FS {Disarmed}

[jorge luis]

Hi Carolina
 
You simply need to add the path  ‘your FS installation dir/freesurfer/matlab’ 
to the search path in Octave:
 
addpath(‘your FS installation dir/freesurfer/matlab’);
 
For example, to build a histogram of cortical thickness values for the first 
subject of your study,  you can try:
 
thickness_data = squeeze(load_mgh(‘lh.thickness.mgh’));
hist(thickness_data(:,1));
 
where lh.thickness.mgh contains the thickness data for the left hemisphere of 
your subjects (eg.. those generated with mris_preproc)
 
Cheers 
 
Jorge

--- El jue, 7/7/11, Carolina Valencia  escribió:


De: Carolina Valencia 
Asunto: Re: [Freesurfer] Matlab and FS
Para: "jorge luis" 
CC: freesurfer@nmr.mgh.harvard.edu
Fecha: jueves, 7 de julio, 2011 15:30


Hi Jorge,
Thanks for your reply,  I installed Octave in the Ubuntu machine, Should I 
setup something in order to use the FS commands?
Best regards,
Carolina


2011/7/5 jorge luis 





  
Hi Carolina 
  
There is a directory freesurfer/matlab which contains several matlab-based 
scripts for reading and writing (after modified) surface- and volume-based data 
generated in freesurfer. 
Transport files from Linux to Windows will be tedious and things may not work 
properly, therefore, I recommend you to install Matlab for Linux or you can try 
with Octave (a kind of GNU Matlab for Linux). 
  
Cheers 
Jorge

--- El mar, 5/7/11, Carolina Valencia  escribió:


De: Carolina Valencia 
Asunto: [Freesurfer] Matlab and FS
Para: freesurfer@nmr.mgh.harvard.edu
Fecha: martes, 5 de julio, 2011 17:39





Hello FS'users,

I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but 
the problem is that I have Installed matlab in a computer (windows) and FS in 
another one (ubuntu)
Can I configure something to use the FS commands in matlab in order to obtain 
some graphs?
And also, where can I find the cortical thickness in each regions (Brodmann 
areas, gyrus or sulci) of the brain in order to compare a normal patient with a 
patiwnt who has a cortical dysplasia ?

Thanks a lot for your help,

Carolina


-Adjunto en línea a continuación-


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-- 
-- 
Carolina Valencia Muñoz
Bioingeniera
LINK DIAGNOSTICO DIGITAL SA
Cel: 3016411824
Of: (4) 444 54 65 

-Adjunto en línea a continuación-


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Re: [Freesurfer] talaraich ERROR

[Douglas N Greve]

Yep, use
tkregister2 --s subject --fstal
there are instructions in the trouble shooting tutorial on the wiki.
doug

Carolina Valencia wrote:
> Hi FSexperts,
>
> I have a case of a child with  /Hydrocephalus and cortical dysplasia, 
> the patient has a subcutaneous ventriculo-peritoneal shunt that 
> produces an artifice in all MRI sequences, I try to recon-all but it 
> exit with ERROR/
> #
> #@# Talairach Failure Detection Thu Jul  7 11:03:21 COT 2011
> /home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri
>
>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
>
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0., pval=0. < threshold=0.0050)
> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae 
> #54-Ubuntu SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux
>
> recon-all -s hptu_vol04 exited with ERRORS at Thu Jul  7 11:03:21 COT 2011
>
> is possible to process it in automated fashion? 
>
> Thanks,
>
> Best regards,
>
> Carolina
> 
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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

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Re: [Freesurfer] Error with Tksurfer

[Bruce Fischl]

Hi Antonella,

did bert inflated look ok on the other computer? Usually this problem 
goes away if you update the video card driver.


cheers
Bruce
On Thu, 7 Jul 2011, Antonella 
Kis wrote:



Good afternoon Bruce,

I am still trying to fix my error related to the surface image display when 
using tksurfer bert lh inflated. As you saw the image looks weird and what I in 
the mean time I
tried something: I save the weird surface displayed by that computer using SAVE 
SURFACE AS and I transfers this file nsmed by me lh.bertsurf to another 
computer. When I
looked on the image using
 tksurfer bert lh bertsurf, the surface that came up was exactly like the bert 
lh inflated should be, having the same number of vertices and faces. Can you or 
somebody else
give me some advice on what to do so I can get the same display on the other 
computer? Seems that everything is well calculated just the surface 
display/image is looking
weird on that computer. What can be the problem? I attached the saved surface from the 
computer where it looked weird so the called "weird surface".

Also can I save a surface and loaded in freesurfer but not as a tiff image? 
What's the best way to save my volumes and/or surfaces?

Thank you very much for your help.
Antonella




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[Freesurfer] preprocessing qc

[Chindhuri Selvadurai]

Best,

Chindhuri Selvadurai

 Psychiatric Neuroimaging, Manoach Lab
 Martinos Center for Biomedical Imaging, MGH
 Phone: (617)726-0307
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Re: [Freesurfer] more on fieldsign problems-

[Michelle Umali]

Hi Doug,
The eccen and polar maps look ok, although activation tends to be  
limited to the occipital poles and lateral surface not really along  
the calcarine.

Is it possible to find out how the colors in the eccen and polar  
images correspond to positions in the stimulus using rtview?  There's  
no legend.

Thanks.
Michelle



Quoting Douglas N Greve :

> Hi Michelle, do the eccen and polar maps look ok? Also, I would
> probably smooth them a little bit. The field sign calculation is
> basically a spatial derivative so it can be sensitive to noise.
> doug
>
> Michelle Umali wrote:
>> Dear all,
>>  I've been having issues with my fieldsign images all I get are
>> speckles. I did the following and did not get any errors:
>>
>> 1) ran recon-all -all
>> 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
>> 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d   
>> rh.occip.patch.flat
>> 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy  
>>  48 paradigm
>> rtopy.par -nskip 4 fwhm 0
>> 5) selxavg3-sess -a rtopy.self.rh -s sj09
>> 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
>>
>> When I looked at the fieldsign map using:
>> 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
>>
>> all I got were blue and red speckles.  The polar and eccentricity   
>> maps seemed ok.
>>
>>
>> Any help would be great.
>>
>> Michelle
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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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>
>
>
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[Freesurfer] QC Montages error

[Chindhuri Selvadurai]

I am getting an error when using a script that combines these 3 actions:

preproc.sh
std_map_qc_montages.bash
put_tpef.bash


Freesurfer version 4
SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects
Script:
/cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh

It looks like the preproc-sess finishes okay, but the problem starts
afterwards, but I'm not sure how to fix this easily.. it looks like it's
looking for files that aren't there, but I haven't gotten this error
before.

Thanks!

Output, with error at end:

- mkbrainmask Done -

Thu Jul  7 17:15:21 EDT 2011
mkbrainmask-sess done

Started at Thu Jul 7 16:54:00 EDT 2011
Ended   at Thu Jul  7 17:15:21 EDT 2011
preproc-sess done
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
mri_convert f.nii fskip8.nii --nskip 8
nskip = 8
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.76, -0.00683426, -0.00130865)
j_ras = (0.0069578, -0.984569, -0.174858)
k_ras = (-9.34106e-05, -0.174863, 0.984593)
Skipping 8 frames
writing to fskip8.nii...
bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
such file or directory
cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or
directory
cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or
directory
cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or
directory
bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
such file or directory
cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or
directory
cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or
directory
cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or
directory
bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
such file or directory
cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or
directory
cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No such file or
directory
cp: cannot stat `./013/lightboxes/tmean_lightbox.png': No such file or
directory
bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
such file or directory
cp: cannot stat `./015/lightboxes/tsnr_lightbox.png': No such file or
directory
cp: cannot stat `./015/lightboxes/tstd_lightbox.png': No such file or
directory
cp: cannot stat `./015/lightboxes/tmean_lightbox.png': No such file or
directory
bash: /space/ventz

Re: [Freesurfer] more on fieldsign problems-

[Bruce Fischl]

are you sure it's registered well to the anatomical/surface?
On Thu, 7 Jul 
2011, Michelle Umali wrote:

> Hi Doug,
> The eccen and polar maps look ok, although activation tends to be
> limited to the occipital poles and lateral surface not really along
> the calcarine.
>
> Is it possible to find out how the colors in the eccen and polar
> images correspond to positions in the stimulus using rtview?  There's
> no legend.
>
> Thanks.
> Michelle
>
>
>
> Quoting Douglas N Greve :
>
>> Hi Michelle, do the eccen and polar maps look ok? Also, I would
>> probably smooth them a little bit. The field sign calculation is
>> basically a spatial derivative so it can be sensitive to noise.
>> doug
>>
>> Michelle Umali wrote:
>>> Dear all,
>>> I've been having issues with my fieldsign images all I get are
>>> speckles. I did the following and did not get any errors:
>>>
>>> 1) ran recon-all -all
>>> 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
>>> 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d
>>> rh.occip.patch.flat
>>> 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy
>>>  48 paradigm
>>> rtopy.par -nskip 4 fwhm 0
>>> 5) selxavg3-sess -a rtopy.self.rh -s sj09
>>> 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
>>>
>>> When I looked at the fieldsign map using:
>>> 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
>>>
>>> all I got were blue and red speckles.  The polar and eccentricity
>>> maps seemed ok.
>>>
>>>
>>> Any help would be great.
>>>
>>> Michelle
>>> ___
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>
>
>
> ___
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>
>
>
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[Freesurfer] question about qdec

[ZhiLiangLong]

Hi all:
I have three groups of subjects (major depression disorder,slight 
depression disorder and contrast),i want to use qdec to obtain the statistical 
significant areas containing difference of cortical thickness  measurment among 
them. But there are some errors appearing when i run the group analysis:

 ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels

 I think the error is related to the diagnosis.levels file which has 3 
levels because i can run it successfully after removing any one of them.But i 
don't know why.
Can you give me some help or suggestions?
   I have saved error information into the error.log file(see attachments)
HP 
MD 
DXReading /usr/local/freesurfer/lib/tcl/tkUtils.tcl 
 
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl 
 
Loading data table qdec.table.dat... 
Number of columns:  4 
fsid column:1 
Number of factors:  3 
Number of subjects: 59 
Reading discrete factor levels from config file ./sex.levels 
'Male','Female', done 
Reading discrete factor levels from config file ./diagnosis.levels 
'HP','MD','DX', done 
 
Data table qdec.table.dat loaded. 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n001_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d20' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n003_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd01' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n004_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d02' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n005_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd07' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n009_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd30' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n011_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd15' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n012_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_19' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n013_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d21' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n014_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d28' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n015_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d22' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n016_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d10' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n017_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d11' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n019_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d16' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n020_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd04' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n021_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d14' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n022_3_a' in 
SUBJECTS_DIR 
sh: Syntax error: Bad fd number 
ERROR: QdecProject::VerifySubjects: Couldn't fi

[Freesurfer] Creation of normalized cortical regions of interest

[汪贵宏]

Hi,freesurfers:
 
Recently,I read a paper which used freesurfer to processed their data,this 
is the paper's 
link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159
In this paper,the antor said :
"One of the critical steps of the whole procedure was to partition the 
participants' cortex into ROIs located in an identical topographic position for 
each participant despite interindividual anatomical variation. We used 
Freesurfer to register a labeled mesh from an average brain onto the brain of 
each individual participant, where each label corresponded to one of 66 
anatomical cortical regions . This output provided for every participant a 
standardized partition of the cortex into 66 regional areas. In a second step, 
each of these regional areas were subdivided on the Freesurfer average brain 
into a set of small and compact regions of about 1.5 cm2, resulting in 998 ROIs 
covering the entire cortex. This subdivision was then registered on the 
individual brain using the same transformation as for the 66 regional areas 
thus maintaining the topological constraints of mapping. Consequently, the 
resulting partitions of the cortex into 66 and 998 ROIs were in anatomically 
closely matched positions for all participants "
 
So,I wander how can we subdivided the 66 ROIs into 998 ROIs?
 
Thanks,
wang
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[Freesurfer] A question about the Freesurfer version compatibility of Tracula

[Shanqing Cai]

Hi,

I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer.
However, my data set are processed with the recon-all of an earlier version of
FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the
subjects in the data set with 5.1.0. Would running Tracula on 5.0.0
reconstructions cause any problems that render the results unusable/not
trustable?

Thank you!

Best,
Shanqing Cai


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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