Re: [Freesurfer] Tracula Error -preproc Segmentation fault (core dumped)

[Anastasia Yendiki]

Hi Kristina - I suspect there's some misregistration, or part of the brain 
mask (and hence the anatomical segmentation) missing or something like 
that. Do you mind uploading the tracula directories of this subject for me 
to take a look at?


https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks!

a.y

On Thu, 1 Sep 2016, Kristina Jelinkova wrote:



Hello everyone,


I've been using Tracula for a while now with much success (and help from the
archive) but I've run into an error I haven't been able to solve. I have
several subjects for which trac-all -preproc ends with Segmentation fault
(core dumped) 


I don't think it's a mistake with my directories, they appear correct and
I've ran numerous subjects successfully like this already. The dti data and
aparc+aseg also appear normal. I'm attaching the trac-all log and error log
from one of these problematic subjects. Any insight would be greatly
appreciate!


Thank you, 


Kristina Jelinkova


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Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

[Bruce Fischl]

Hi Ben

are the bright points segmented as wm in the wm.mgz? If so, you might try 
erasing them and rerunning


cheers
Bruce
On Wed, 31 Aug 2016, Benjamin Baird wrote:


Dear Freesurfer experts,

We are currently working with some scans that were collected on a GE 3T
scanner. The goal is to analyze cortical thickness. The scans seem to be
relatively high quality with the exception that there are what appear to be
inhomogeneities in the intensity of the gray matter (appears too bright in
places), which is causing the WM to extend/jump into cortex (see attached
image). We're wondering if there are any parameter adjustments to recon that
might help with this as the errors occur frequently enough that fixing them
all manually will be fairly cumbersome. This type of error doesn’t seem to
be discussed very much in the available information on freesurfer quality
control as far as we’ve seen. Thanks in advance for any thoughts
recommendations or advice you might be able to offer.

Best regards,
Ben

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[Freesurfer] Multi-band slice timing correction

[Wang, Ruosi]

Dear Freesurfer developers:

I'm seeking out ways for performing multi-band slice timing correction
with freesurfer 5.3. I've searched the mailing list, and noticed that there
might be a couple of ways for doing this. But, I still have some conerns
for different ways, and please see below for my questions:

1) using new version of stc.fsl and slicedelay

I tried to download these files from a link provided in an emai loop
 of
the mailing archive, but failed to do so. Could you please share the
updated downloading link to these files. In addition, what kinds of
information shall I provide?  The slice order and number of SMS slice
groups?

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fslftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/slicedelay


2) using freesurfer 6 for preprocessing
Since freesurfer 6 is still in beta version, can I use the proproc-sess of
fs6 for data preprocessing only and switch to fs 5.3 afterwards for all the
other anlaysis? Is there any downside for this, in comparison with just
using the new version of stc.fsl and sliceday?

In addition, for the input file so of -sliceorder, shall it be the slice
number ordered by time? And for the input file of -ngroups, shall it be the
number of slices that are colloected at the same time?

Thank you so much, it is deeply appreciated.
Best,
Ruosi

-- 
Ruosi Wang
Graduate Student
Vision Lab in Psychology Department
Harvard University
William James Hall, 7 floor
33 Kirkland Street
Cambridge, MA 02138
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[Freesurfer] nu_correct crashed

[Fanny Munsch]

Hi everyone,

I just installed the latest version of Ubuntu (Ubuntu 16.04 LTS) and I 
reinstalled FreeSurfer (centos4). When I computed recon-all it exited with 
errors (nu_correct crashed). I have attached the .log files. I have already 
used FreeSurfer with older versions of Ubuntu and I have never had this error.

Do you have any idea what needs to be done?

Thanks a lot

-
Fanny Munsch

PhD in Neurosciences
Engineer in MRI post-processing


mri_nu_correct.mni.log
Description: mri_nu_correct.mni.log


orig_nu.log
Description: orig_nu.log
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Re: [Freesurfer] 3 fixed factors and matrix design

[Anderson M. Winkler]

Hi Shady,

Try assembling the design as this:

EV1: Group 1 (coded as 0/1)
EV2: Group 2 (coded as 0/1)
EV3: Group 3 (coded as 0/1)
EV4: Sex (coded as +1/-1)
EV5: Site (coded as +1/-1)

The contrasts to compare the three groups are then:
C1: [1 -1 0 0 0]
C2: [1 0 -1 0 0]
C3: [0 1 -1 0 0]
C4: [-1 1 0 0 0]
C5: [-1 0 1 0 0]
C6: [0 -1 1 0 0]

>From the description it seems site and group are confounded, although not
completely, such that it should be possible to still draw some inferences,
although without much power.

The above does not include terms for interactions. If it's something you
could be interested in, then extra EVs can be added.

All the best,

Anderson


On 30 August 2016 at 11:40, Shady Rahayel  wrote:

> Greetings,
>
> I want to design a matrix that contains 3 fixed factors. The first is
> diagnosis (3 levels), the second is gender (2 levels), and the last is
> imaging site (2 levels). However, the thing is that the imaging site factor
> only applies to only one level of the diagnosis factor (i.e. patients from
> the first level of the diagnosis factor were seen in 2 different imaging
> sites, whereas for the two other groups of patients the same imaging site
> was used).
>
> I have followed the tutorials but I still be am confused concerning how I
> should go about creating the design matrix with 3 fixed factors. Would it
> be:
>
> GroupDescriptorFile 1
> Title xx
> Class Diagnosis1-Male-Site1
> Class Diagnosis1-Female-Site1
> Class Diagnosis1-Male-Site2
> Class Diagnosis1-Female-Site2
> Class Diagnosis2-Male-Site1
> Class Diagnosis2-Female-Site1
> Class Diagnosis3-Male-Site1
> Class Diagnosis3-Female-Site1
> Inputetc etc...
>
> Afterwards, if I'm looking for a difference between Diagnosis1 and
> Diagnosis2, what would be the contrast?
> 0.25 0.25 0.25 0.25 -0.5 0.5 0 0 ?
>
> Thank you very much for your help,
>
> Shady
>
> --
> *Shady Rahayel*
> Étudiant au Ph.D. en neuropsychologie R/I
> Université du Québec à Montréal
>
> Centre d'Études Avancées en Médecine du Sommeil
> Hôpital du Sacré-Coeur de Montréal
>
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[Freesurfer] Fwd: mri_glmfit: Cannot allocate memory

[Heidi Foo]

Dear FreeSurfer team,

I apologize for posting this again.

I tried to run glm_fit to fit group membership. For this model, I have 3
diagnostic groups namely, HC, MCI, AD, and added lobar (Frontal, Parietal,
Occipital, Temporal) WMH as the covariates.

My contrasts are as follow:
Group membership: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 -1 0 0 0 0 0 0 0 0 0
0 0 0
Frontal/Parietal/Occipital/Temporal MCI_HC: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0
Frontal/Parietal/Occipital/Temporal MCI_AD: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0
Frontal/Parietal/Occipital/Temporal AD_HC: 0 0 0 -1 0 1 0 0 0 0 0 0 0 0 0

However, I got the error message "MatrixReadTxt: could not scan value
[1][1]; MATFILES: 0 x 0, type 0, imagf 0, name ' '; unsupported matlab
format 0 (unknown).

My command is:
mri_glmfit --glmdir
lh.thickness.regress.covariates.sm15.glmdir/group_membership --y
./lh.thickness.regress.convariates.sm15.glmdir/eres.mgh --X
./membership_group_all.mat --C ./membership_group.txt --C
./membership_Frontal.txt --C ./membership_MCI_HC_Frontal.txt --C
./membership_MCI_AD_Frontal.txt --C ./membership_AD_HC_Frontal.txt --C
./membership_Parietal.txt --C ./membership_MCI_HC_Parietal.txt --C
./membership_MCI_AD_Parietal.txt --C ./membership_AD_HC_Parietal.txt --C
./membership_Occipital.txt --C ./membership_MCI_HC_Occipital.txt --C
./membership_MCI_AD_Occipital.txt --C ./membership_AD_HC_Occipital.txt --C
./membership_Temporal.txt --C ./membership_MCI_HC_Temporal.txt --C
./membership_MCI_AD_Temporal.txt --C ./membership_AD_HC_Temporal.txt --surf
fsaverage lh --cortex --fwhm 0


I am not sure what went wrong, any help will be great.

Many thanks,
Heidi
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