Re: [Freesurfer] units for tracula output

[Yendiki, Anastasia]

Hi Jim - Units of diffusivity are mm^2 / sec.


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Thursday, May 9, 2019 4:33:27 PM
To: Freesurfer support list
Subject: [Freesurfer] units for tracula output


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What units are the diffusion measures generated by tracula that are found in  
the files named

“pathstats.overall.txt”. For example, as 10^-3



Jim





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Re: [Freesurfer] Tracula error -path

[Yendiki, Anastasia]

Hi Lorenzo - If you are still having this problem, please send the trac-all.log 
file from one of the 4 subjects.


a.y



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lorenzo Pini 

Sent: Friday, May 10, 2019 4:35:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error -path


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Hi list,

Im using TRACULA in a dataset of 60 subjects.
for 56 subjects everything is fine, but for 4 subjects I had the following 
error:
>> ncpts: Subscript out of range.

For these subjects TRACULA does not reconstruct the file 
dpath/merged_avg33_mni_bbr.mgz and the statistics of the tracts (i.e. 
pathstats.* files)
Freesurfer parcellations look fine

Do you have any suggestions?
Thank you
Lorenzo
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[Freesurfer] multi-slice timing correction

[Joseph Dien]

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Hi Doug,
   I’m happy to see that FreeSurfer6 provides enhanced support for slice 
timing.  I’m trying to run it on some multi-slice data.  May I ask you for some 
guidance on how to use the new preproc-sess options?  As I understand it, I 
would specify “-ngroups 10” because the data were collected in ten groups of 
six slices at a time?  I’m not sure how to specify “-sliceorder”.  Slice times 
are below.  Thanks for any help you can provide.

Joe

0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000
0
877.5000
502.5000
125
1005
627.5000
252.5000
1130
752.5000
377.5000



Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://joedien.com

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[Freesurfer] Cluster-wise multiple comparison correction

[Jacobs, H (NP)]

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Hi all!

I would love to use the cluster-wise multiple comparison correction method in 
FS 6.0 for our PET data (in fsaverage space and smoothed).
However, since we have some complex models, I did the statistical analyses in R 
and then converted this to a surface overlay map in mgh format (in log10 
p-values).
That means that I don’t have the typical glm output that is usually obtained in 
Freesurfer.
I tried to run the mri_glmfit-sim function, but it does need the mri_glmfit.log 
file.
Is there a way around this?

Many thanks!
Heidi
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Re: [Freesurfer] selxavg3-sess failed

[Greve, Douglas N.,Ph.D.]

It does not look like the error was captured in the log file. Can you send the 
full terminal output?
On 6/2/2019 5:02 AM, starxifd wrote:

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Hi, FS experts
I got into trouble when running  ’selxavg3-sess’ with a session id file. All 
sessions specified in sessid file. To do 1st-level GLM analysis, I used the 
following command:
Selxavg-sess -sf sessid -analysis stereo.sm5.lh
Then I was told “Matlab is exiting because of fatal error …… 
ERROR:fast_selxavg3() failed\n”  The log is attached in the mail.
However, I run selxavg3-sess with only one session successfully. (Command: 
Selxavg3-sess -s HC025 -analysis stereo.sm5.lh)
I wonder if there was something wrong with my Matlab (version R2014b) or other 
procedures?
Any advice will be appreciated! Thx!

The whole procedure I did:
preproc-sess -sf sessid -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 
5 -per-run
mkanalysis-sess -fsd bold -analysis stereo.sm5.lh -surface fsaverage lh -fwhm 5 
-paradigm stereo.par -event-related -spmhrf 0 -refeventdur 16 -polyfit 2 
-mcextreg -nskip 4 -TR 2 -nconditions 2 -per-run
mkcontrast-sess -analysis stereo.sm5.lh -contrast 3d-v-non3d -a 1 -c 2
Selxavg-sess -sf sessid -analysis stereo.sm5.lh
Star



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Re: [Freesurfer] FS recon-all issue "if: missing file name"

[Greve, Douglas N.,Ph.D.]

can you send the command line and full terminal output? Also, when you run it 
again, put -debug as the first argument. It will create a huge amount of 
terminal output, but it will be helpful for diagnosing the problem

On 6/2/2019 3:57 AM, Kavinash Loganathan wrote:

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Dear freesurfer, I am following the installation test as suggested 
(http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am currently 
stuck at example 2. When I ran recon-all, I got the output: "if: missing file 
name".

I noticed this has been brought up before, but no solution was provided.

Any suggestions? Thank you.

Kavinash





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[Freesurfer] FS recon-all issue "if: missing file name"

[Kavinash Loganathan]

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Dear freesurfer, I am following the installation test as suggested (
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am
currently stuck at example 2. When I ran recon-all, I got the output: "if:
missing file name".

I noticed this has been brought up before, but no solution was provided.

Any suggestions? Thank you.

Kavinash
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