Re: [Freesurfer] trac-all -stat

[Versace, Amelia]

Thanks, Anastasia!!
It should be it. I had run the same command before with slightly fewer subjects 
in my "set subjlist" and it did work fine. Then I rerun the -path (and added 
extra 18 subjects) to update the tracts with the recent implementation that you 
have done (FS 6). After, started having this issue with -stat However, I 
ended up running the dmri_group after manually creating the *inputs.txt files 
and it did work fine... ;-)
Thanks, Amelia

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 12, 2017 5:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all -stat

Hi Amelia - This means that it can't find any of the tracts that you've 
specified (or any tracts period, if you haven't specified a list) for the 
subjects that you've specified in your config file. It'd be looking under:

/data/dprojects/BIOS/tracula/$subj/dpath/

Best,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia 
[versa...@upmc.edu]
Sent: Wednesday, April 12, 2017 5:00 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -stat

Hi Anastasia,

I am having some issues with the -stat option. Below is the error. I am not 
sure of what's causing the issue. Any idea?
Thanks a lot!! Amelia

-
trac-all -c scripts/dmrirc.stats -stat

INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer
INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME 
/data/software/freesurfer6
ERROR: no pathway reconstructions found
-

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[Freesurfer] trac-all -stat

[Versace, Amelia]

Hi Anastasia, 

I am having some issues with the -stat option. Below is the error. I am not 
sure of what's causing the issue. Any idea?
Thanks a lot!! Amelia

-
trac-all -c scripts/dmrirc.stats -stat

INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer
INFO: Diffusion root is /data/dprojects/BIOS/tracula
Actual FREESURFER_HOME /data/software/freesurfer6
ERROR: no pathway reconstructions found
-

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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Versace, Amelia]

Hi,
I am having the same issue.
Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
Thanks a lot, Amelia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, February 10, 2016 10:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x

what is your command line? I think there is a rescaling in which it expcts the 
phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) scanner. 
Could that be the problem?

On 2/10/16 10:40 PM, Joseph Dien wrote:
I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced 
the existing script.  It did indeed fix the version incompatibility with FSL 
5.x.

I ran into a new problem where it was aborting.  After some trouble shooting 
and looking over the documentation, I realized that --epi is a required input 
without which the script crashes (or is it supposed to be optional but there is 
a bug in the script?).

After including it, it ran much further but then aborted with the following 
error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I'm not sure why the phase image 
exceeds the range though.

It ran without problems with SPM's FieldMap Toolbox and it is from a standard 
Siemen's scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems 
to have exactly double the required range?

Joe

On Nov 26, 2014, at 21:36, Douglas Greve 
> wrote:


It is there again. I don't know what the status if it  is in terms of the 
version. Try it and let me know
doug
On 11/25/14 4:34 PM, Morgan Hough wrote:
Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I don't see it at 
the link in the archives:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old script just 
be changed to accept 5.x version numbers.

Cheers,

-Morgan

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dispose of the e-mail.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com





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[Freesurfer] [Tracula] pathstats.byvoxel.txt for between-group or correlational analyses

[Versace, Amelia]

Dear Anastasia and Tracula experts,
I would like to run between-group statistics using the pathstats.byvoxel.txt 
outputs. It is clear from the website how to manage the NANs. However, what 
would you suggest to use for between-group or correlational analyses? Is there 
a script/function/statistical package in tracula that can handle this kind of 
data?
Thanks a lot, Amelia

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[Freesurfer] network analysis in tracula

[Versace, Amelia]

Dear Anastasia,
Is there a way to get connectivity matrices using the outputs of tracula? 
Thanks a lot, Amelia

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Re: [Freesurfer] Tracula: missing or incomplete tracts

[Versace, Amelia]

Ops... I did not see these replies before! Thank you, both!!
Christopher, the command line works great. I also found the --viewport and the 
--ss, which is exactly what I was looking for! 
I will try the dev version that Anastasia suggested. 
Thanks a lot, Amelia

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Watson, Christopher
Sent: Tuesday, March 17, 2015 9:33 PM
To: Freesurfer support list; Ruopeng Wang
Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts

What about:
freeview -v FA.nii.gz -v V1.nii.gz:vector=yes


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, March 17, 2015 11:57 AM
To: Freesurfer support list; Ruopeng Wang
Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts

Hi Amelia - Sorry, not that I know of. Perhaps this can be a feature request 
for Ruopeng to add to freeview :)

BTW, freeview in 5.3 had a bug with the vector display for some input image 
orientations, but this has been fixed in the dev version (that you can download 
on the web site).

a.y

  On Thu, 12 Mar 2015, Versace, Amelia wrote:

 Dear Anastasia,
 I was wondering if there is a way to automatically (in command line) derive 
 the FA/V1 vector image.
 fslview FA.nii.gz V1.nii.gz   allows to load the FA and V1 image, but then 
 manual section of the (lines) is needed.
 freeview -dti V1 FA   does it too (with different xyz convention), 
 but the 'display as vectors' needs to be manually checked.
 Is there any way to produce this image using command line only? Thanks 
 a lot!! Amelia

 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia 
 Yendiki
 Sent: Friday, March 06, 2015 6:56 PM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts


 Hi Eileen - It looks like there was a A-P flip introduced to your gradient 
 vectors. (See screenshot of the tensor eigenvectors. Because they look right 
 in the coronal view but wrong in the sagittal and axial views, that's why I'm 
 assuming the flip is in the A-P direction.) To fix this you need to multiply 
 the y coordinate of your gradient vectors with -1 and rerun.

 If there are still any cases of missing tracts, please look at the bottom of 
 your dmrirc file for instructions on how to use the reinit parameter (or 
 search for previous emails on that parameter in the archives).

 Note that your DWI voxel size is anisotropic (finer resolution in x/y than 
 z), this may cause bias in tractography, so I'd recommend that you switch to 
 isotropic resolution for future acquisitions if you have control over it.

 Hope this helps,
 a.y

 On Fri, 27 Feb 2015, Eileen Moore wrote:

 Hi Anastasia,

 Sorry for the delay -- I missed your response.  I did look at the 
 anatomical segmentations and thought they looked OK. I've uploaded 
 the tracula and corresponding freesurfer data for two subjects: one with 
 complete tracts and one with missing/incomplete tracts. I also uploaded my 
 dmrirc file. Thanks for taking a look for me.

 Eileen.



 Hi Eileen - Have you checked the anatomical segmentations of the 
 subjects? The mask that's used by default is the aparc+aseg_mask, 
 which comes from registering the cortical parcellationg and subcortical 
 segmentation from T1 to diffusion space, and then dilating it by a couple of 
 voxels.

 If you upload an example data set for me here, I can take a look:
 
 https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.har
 vard.edu_filedrop2_d=BQIDaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
 pxeFUr=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq
 5C4m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbMs=TVmCtWOX7TmzlQhiV
 JibKKVtj6CQczyAkyupGnmGZa0e= Please include all tracula-related 
 directories of the subject (dmri, dlabel, etc).

 Thanks!
 a.y

 On Thu, 18 Dec 2014, Eileen Moore wrote:

 Hi - I'm having difficulty with missing or incomplete tracts most of 
 my subjects. I'm hoping for suggestions on where I can look for data 
 problems.  The majority of my subjects have at least one 
 missing/incomplete tract, but the specific problematic tract varies 
 across subjects (e.g., one subject has a missing L.Uncinate; another 
 subject has a missing Forceps Major; another is missing the ILF 
 bilaterally, etc.).  For my problematic tracts, the path.pd.nii.gz is 
 a single line/curve rather than the diffuse volumetric distribution.
 I'm not sure how to correct this.

 I have checked my eigenvectors -- the lines appear to be pointing in 
 the correct directions in my dtifit_V1 -- so I believe my gradient 
 table is correct

 I've checked my images for motion via visual inspection and by 
 excluding any subjects with dwi_motion

Re: [Freesurfer] Tracula: missing or incomplete tracts

[Versace, Amelia]

Dear Anastasia,
I was wondering if there is a way to automatically (in command line) derive the 
FA/V1 vector image.
fslview FA.nii.gz V1.nii.gz allows to load the FA and V1 image, but then 
manual section of the (lines) is needed. 
freeview -dti V1 FA does it too (with different xyz convention), 
but the 'display as vectors' needs to be manually checked. 
Is there any way to produce this image using command line only? Thanks a lot!! 
Amelia

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, March 06, 2015 6:56 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts


Hi Eileen - It looks like there was a A-P flip introduced to your gradient 
vectors. (See screenshot of the tensor eigenvectors. Because they look right in 
the coronal view but wrong in the sagittal and axial views, that's why I'm 
assuming the flip is in the A-P direction.) To fix this you need to multiply 
the y coordinate of your gradient vectors with -1 and rerun.

If there are still any cases of missing tracts, please look at the bottom of 
your dmrirc file for instructions on how to use the reinit parameter (or search 
for previous emails on that parameter in the archives).

Note that your DWI voxel size is anisotropic (finer resolution in x/y than z), 
this may cause bias in tractography, so I'd recommend that you switch to 
isotropic resolution for future acquisitions if you have control over it.

Hope this helps,
a.y

On Fri, 27 Feb 2015, Eileen Moore wrote:

 Hi Anastasia,
 
 Sorry for the delay -- I missed your response.  I did look at the 
 anatomical segmentations and thought they looked OK. I've uploaded the 
 tracula and corresponding freesurfer data for two subjects: one with complete 
 tracts and one with missing/incomplete tracts. I also uploaded my dmrirc 
 file. Thanks for taking a look for me.
 
 Eileen.
 
 
 
 Hi Eileen - Have you checked the anatomical segmentations of the 
 subjects? The mask that's used by default is the aparc+aseg_mask, 
 which comes from registering the cortical parcellationg and subcortical 
 segmentation from T1 to diffusion space, and then dilating it by a couple of 
 voxels.
 
 If you upload an example data set for me here, I can take a look:
 https://gate.nmr.mgh.harvard.edu/filedrop2/
 Please include all tracula-related directories of the subject (dmri, dlabel, 
 etc).
 
 Thanks!
 a.y
 
 On Thu, 18 Dec 2014, Eileen Moore wrote:
 
 Hi - I'm having difficulty with missing or incomplete tracts most of 
 my subjects. I'm hoping for suggestions on where I can look for data 
 problems.  The majority of my subjects have at least one 
 missing/incomplete tract, but the specific problematic tract varies 
 across subjects (e.g., one subject has a missing L.Uncinate; another 
 subject has a missing Forceps Major; another is missing the ILF 
 bilaterally, etc.).  For my problematic tracts, the path.pd.nii.gz is 
 a single line/curve rather than the diffuse volumetric distribution.  
 I'm not sure how to correct this.
 
 I have checked my eigenvectors -- the lines appear to be pointing in 
 the correct directions in my dtifit_V1 -- so I believe my gradient 
 table is correct
 
 I've checked my images for motion via visual inspection and by 
 excluding any subjects with dwi_motion outliers in AvgTranslation, 
 AvgRotation, PercentBadSlices, and AvgDropoutScore.
 
 I inspected the nodif_brain_mask.nii.gz  to look for chunks of missing 
 brain and did not identify any problems here.
 
 I've tried increasing the number of control points for each tract.
 
 I'd very much appreciate any suggestions on how to troubleshoot next.
 
 Thank you,
 Eileen.
 
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 and the e-mail contains patient information, please contact the 
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 . If the e-mail was sent to you in error but does not contain patient 
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