Re: [Freesurfer] selxavg3-sess

2019-10-02 Thread Greve, Douglas N.,Ph.D. 
It is having some problems unzipping a nifti file. Does it work on other 
runs/sessions/subjects? If so, then there might be something wrong with that 
file. Alternative, check /var/volders/v3 to see if the disk is filling up.

On 10/1/2019 1:43 PM, Sanati Monfared, Shamsi wrote:

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Hi all,

I am running the functional analyses (selxavg3_sess) and stuck at the following 
error, which I have no idea what to do (apparently the analyses have been OK up 
until run 010 and the error happened in run 012). I received the same errors in 
my all subjects (at run 012)


 'gunzip -c 
/Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/010/fmcpr.up.sm5.fsaverage.lh.nii.gz
 > 
/var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tp7da06091_16b6_41ba_8283_005c005b5dd3.load_nifti.m.nii'



cmd =


'gunzip -c 
/Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/012/fmcpr.up.sm5.fsaverage.lh.nii.gz
 > 
/var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tpc5683b1b_4f0b_4593_ab5d_82233348f546.load_nifti.m.nii'


ERROR: fast_st2fir: two or more presentations are simultaneous

ERROR: creating FIR design matrix for Condition03

Dot indexing is not supported for variables of this type.


Error in flac_customize (line 358)

if(~isempty(flacnew.TFmtx))


Error in fast_selxavg3b (line 184)

flac = flac_customize(flac);



>> --

ERROR: fast_selxavg3() failed\n


Any advice would be highly appreciated!

Thanks,

-Shamsi









---



[cid:part1.6E14BA9C.DE251743@mgh.harvard.edu]
Wheeler Lab | Center for Advanced Brain 
Imaging

831 Marietta St NW, Atlanta, GA 30318

Email: smonfar...@gatech.edu

Phone: 205-607-1656



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Re: [Freesurfer] Freesurfer three groups: group A vs C power.

2019-10-02 Thread Greve, Douglas N.,Ph.D. 
The DOF is determined only from the design matrix as
DOF = #RowsX - #ColsX
So, it would be 9 regressors, not 6

On 9/26/2019 12:31 PM, cody samth wrote:

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Hi I have a question regarding how freesurfer calculates the degrees of freedom 
when you have three groups in the FSGD/contrast files but are running analyses 
on group A vs C.

For example I have an analysis with 3 groups and 2 covariates. My primary 
question is: is there a difference between any groups. Which I have the 
contrast:
1 -1 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0

When I write a contrast for A vs C: (1 0 -1 0 0 0 0 0 0) Does freesurfer 
consider this model as 9 regressors? Or 6 regressors; which would be present in 
a typical group 1 vs group 2 analysis that could be modeled by (1 -1 0 0 0 0) 
if group B didn't exist?



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Re: [Freesurfer] Question about using tkregisterfv to check registration

2019-10-02 Thread Greve, Douglas N.,Ph.D. 
Can you run
tkregisterfv --debug --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta
and send the terminal output?

On 10/2/2019 3:58 PM, Vicky Yang wrote:

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Dear Freesurfer experts,

I used mri_coreg to register my pet data to T1 like below:

  mri_coreg --mov pet.nii.gz --ref T1.nii --reg pet_T1.reg.lta

After coregistering, I checked the registration using tkregisterfv like below:

  tkregisterfv --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta

However, the command didn't work with an error:
  if: Expression Syntax.

Any suggestions would be appreciated. Thank you in advance for your help.

Sincerely,
Vicky




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Re: [Freesurfer] username and password

2019-10-02 Thread fsbuild 
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OK, thanks for letting us know. We will look into when/how that 
redirect started to happen. Just to clarify though, you do not need to 
login to the Martinos center to download the freesurfer release binaries or 
source code, i.e., using that form was just to get on the freesurfer mail list.



The Freesurfer 6.0
release binaries (for Linux and MacOS) can be downloaded from,


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





The latest development branch with the freesurfer source code can be obtained 
from GitHub, 


https://github.com/freesurfer/freesurfer



- R.


  

  Rachel S
October 2, 2019 at 15:36
  
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CautionHi,
I
 have the same problem. It directs me to the Martinos Centre Login, 
which never happened before. I've subscribed to the maillist.

Best,Rachel

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fsbuildOctober 1, 2019 at 16:08
  External Email - Use 
CautionHello Takashi,
Did you create a login to the list on this page, 

http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
- and then receive the email notification, and then did you do the confirmation 
step?
- R.
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[Freesurfer] Question about using tkregisterfv to check registration

2019-10-02 Thread Vicky Yang 
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Dear Freesurfer experts,

I used mri_coreg to register my pet data to T1 like below:

  mri_coreg --mov pet.nii.gz --ref T1.nii --reg pet_T1.reg.lta

After coregistering, I checked the registration using tkregisterfv like
below:

  tkregisterfv --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta

However, the command didn't work with an error:
  if: Expression Syntax.

Any suggestions would be appreciated. Thank you in advance for your help.

Sincerely,
Vicky
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Re: [Freesurfer] username and password

2019-10-02 Thread Rachel S 
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Hi,

I have the same problem. It directs me to the Martinos Centre Login, which
never happened before. I've subscribed to the maillist.

Best,
Rachel

fsbuild  于2019年10月1日周二 下午4:09写道：

> External Email - Use Caution
>
> Hello Takashi,
>
> Did you create a login to the list on this page,
>
> http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> - and then receive the email notification, and then did you do the
> confirmation step?
>
> - R.
>
> On Oct 1, 2019, at 11:03, Yamada, Takashi 
> wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I'm subscribers of freesurfer.
> However, I am about to reading the mail exchange about the Q of
> freesurfer,
> I was asked to input the username and password, then I cannot read them.
> How should I proceed for that?
>
> Best,
> Takashi Yamada
>
> 
> Takashi Yamada, MD & PhD
>
> Postdoctorial Research Associate
> Department of Cognitive, Linguistic and Psychological Sciences (CLPS)
> Brown University
> Box 1821  190 Thayer Street  Providence, RI 02912
> TEL : +1 401 863 9488  FAX : +1 401 863 2255
> Email: takashi_yam...@brown.edu
>
> 
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed} {Disarmed}

2019-10-02 Thread Caspar M. Schwiedrzik 
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following up on this: how do we display complex values from a retinotopy
analysis in freeview?
thanks!
caspar


Am Fr., 20. Sept. 2019 um 14:22 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu>:

> Hi Ruopeng and Doug,
> thanks for the hint with the Freeview update. We can now display a linear
> color bar when choosing the color wheel option.
> However, it is not possible to choose "complex", as it was in tksurfer. Is
> Freeview dealing with that internally, or what should we do to display
> results from the retinotopy analyses?
> Thanks,
> Caspar
>
>
> Am Mi., 11. Sept. 2019 um 17:02 Uhr schrieb Ruopeng Wang <
> rpw...@nmr.mgh.harvard.edu>:
>
>> The scalar bar display for overlay in stable 6.0 is broken. If you can
>> install the latest dev build, you should be able to see the scalar bar:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>> 
>>
>> Best,
>> Ruopeng
>> On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote:
>>
>> External Email - Use Caution
>> Hi Doug and Ruopeng,
>> thanks a lot for your advice!
>> Is there a way to display a meaningful legend? In tksurfer/rtview, we get
>> a linear legend that does not seem to make much sense and in freeview we
>> typically do not get anything when we choose color wheel and then click on
>> the legend button.
>> Thanks! Caspar
>>
>>
>> Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu>:
>>
>>> When you run rtview, it will run tksurfer. To get to the color wheel,
>>> open View->Configure->Overlay, then select "Color Wheel" under the
>>> "Color Scale" tab.
>>>
>>> On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hi Doug and Roupeng,
>>> > did you already have the chance to look into the question how to
>>> > display the color wheel with rtview and/or freeview?
>>> > Thank you! Caspar
>>> >
>>> > Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
>>> > >> > >:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hi Doug and Ruopeng,
>>> > it would be amazing if you could dig out the information on how to
>>> > display the color wheel.
>>> > Looking forward to what you find!
>>> > Caspar
>>> >
>>> >
>>> > Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>>:
>>> >
>>> > Hi Caspar, sorry for the delay. I have not used the retinotoy
>>> > stream in a long, long time so I don't know off the top of my
>>> > head. I'll have to look into it. tksurfer (from rtview) does
>>> > have a way to display using the color wheel, but I don't
>>> > remember how to do it.
>>> >
>>> > Ruopeng, can freeview display using a color wheel?
>>> >
>>> > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>> >>
>>> >> External Email - Use Caution
>>> >>
>>> >> Hi!
>>> >> I wanted to ask again whether there is a way to display the
>>> >> color wheel in rtview and/or freeview. We are debugging our
>>> >> analyses and it would be immensely helpful to have a legend
>>> >> that specifies the color assignments.
>>> >> Thank you,
>>> >> Caspar
>>> >>
>>> >> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>>> >> >> >> > wrote:
>>> >>
>>> >> Hi!
>>> >> I am following up on this thread trying to understand how
>>> >> to make the color wheel visible in rtview, or, if
>>> >> necessary, in freeview.
>>> >> Thank you! Caspar
>>> >>
>>> >>
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>>>  <
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=jp7PANwd2YntpsAh9vlW-QSUZFuXwUjqwQh6xScG7bo=d0O8n20UnPtEmd1qaEgrnyVICtHAqvf-ZlhQiv9zNlI=
>>> >
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>>>

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

2019-10-02 Thread Diers, Kersten /DZNE 
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Hi Bronwyn,

thanks for the update and additional info.

I have to say that I have no very good clue at the moment.

Could you maybe upload an examplary file to the Freesurfer FileDrop at 
https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?

Best regards,

Kersten


On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:

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Hi Kersten,

Thank you for your detailed reply and sorry for this delayed response.

Yes the top row in my figure (attached again) was produced by using the 
'--olab' argument with the 'mri_surfcluster' command and then loading each 
cluster from a different label file. I attempted to follow your suggestion and 
adjust the label 'threshold' in Freeview to minimum value in my significance 
map (-5), but this did not display the missing regions - the surface remained 
the same as row 1 of the attached figure.

To provide you with a little more detail about my method - am using 
'mri_surfcluster' with the '--olab' argument to derive all of my significant 
clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each 
label files (from the 'mri_surfcluster' command) back onto the images for each 
of my individual subjects, and then generate subject level stats for each 
cluster using 'mris_anatomical_stats'. At the moment I am concerned that the 
subject level stats I have derived from my label files do not accurately 
represent each significant cluster in totality as regions appear to be missing 
even when i adjust the minimum threshold. As an alternative, when using 
'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments 
for '--olab', and still perform my 'mri_label2label' and 
'mris_anatomical_stats' steps?


Kind regards,


Bronwyn Overs

Research Assistant

[cid:1569997292.6432.28.camel@dzne.de]


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


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From: "Kersten Diers, DZNE" 
To: "Freesurfer support list" 
Sent: Thursday, September 5, 2019 2:13:50 AM
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels


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Hi,

I suppose what we are seeing in the top row of your figure are Freesurfer 
labels, right? I.e. you probably used the '--olab' argument with the 
'mri_surfcluster' command, and are loading each cluster from a different label 
file?

If my speculation is correct, then what you observe could be due to the 
'threshold' setting in freeview, i.e. this little box just below the label box 
in the left part of the GUI.

This threshold is by default set to zero, but lowering it to some sufficiently 
negative value (i.e. the minimum value in the 'sig' map) should also display 
those regions that seem to be missing at the moment.

At least this is what I observed when I tried to reproduce your observation, 
i.e. I could create (and reverse by setting another threshold) similar 
'cut-outs' in the cluster maps.

In addition, you could also load the ouput files that are produced by the 
'--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I 
would guess that they don't show this pattern of missing areas.

Hope this helps,

Kersten


On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:

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Dear Freesurfer mailing list,

I am trying to get to the bottom of a discrepancy between two surface based 
images generated from the output of an LME analysis. The surfaces in row 1 of 
the attached image were generated by loading the four FDR significant clusters 
that were >100mm^2 in the cluster summary file.  The surfaces in row 2 of the 
attached image were generated by loading the significance map generated for the 
same fixed effect (saved from the LME), and thresholding at the FDR corrected 
p-value. The question I have is why are there such large swatches of the 
cortical surface in the row 2 images that are labelled as log10 p = 5, when 
they are not included in the most significant and largest clusters that were 
found in the cluster summary file?


Kind regards,


Bronwyn Overs

Research Assistant

[cid:1569997292.6432.28.camel@dzne.de]


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


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