Re: [Freesurfer] Demeaning variables

[Rodrigo Gonzalez Huerta]

Hey Doug,

Sorry for keep bothering, today I was trying to do what you told me yesterday, 
but some doubts arose. I ran QDEC using DODS to see if there were any 
interactions (significant regions) between age (age variable was not demeaned) 
and group. I didn’t found anything, no significant regions survived monte 
carlo. If that came to happen, you suggested me to use DOSS instead, but… 
because of the characteristics of the disease I’m studying, the slopes 
shouldn’t be similar between patients and controls. My questions are:

1) Can I proceed using DOSS anyway?

2) What if DOSS give me some clusters after running monte carlo? Which is the 
case since I’ve already ran mri_glmfit and obtained three clusters. What should 
I do now? Should I re-run DODS with age-variable demeaned?

3) Since most of my subjects are women (around 80%) and my sample is small (18 
patients, 18 controls), does it have an advantage to remove the males to be 
able to get rid of the gender variable that I’m also regressing out? In order 
to have just two classes (patient and control) instead of four (malecontrol, 
malepatient,….) , or it is better to continue as I’ve been doing, controlling 
for the effect of gender.

Thanks for your help!

Rodrigo



De: freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Douglas Greve 

Enviado: martes, 29 de noviembre de 2016 08:31:20 p. m.
Para: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] Demeaning variables



On 11/29/16 8:52 PM, Rodrigo Gonzalez Huerta wrote:
It makes sense to me, I only have two more questions,

  1.  When you say “see if there are any places where there is an interaction 
between age and group”, do you mean finding significant statistical regions, 
right? And this would be before or after using monte carlo?

After. Even if you have some sig areas, they won't matter if they do not 
overlap with sig areas in DOSS

  1.
  2.  What about using the median or other value instead of the mean since most 
of my subjects are in the range from 20 to 35 years old and only a few in the 
range from 35 to 55 years old. Would this make sense to you?

It has nothing to do with using the mean or median. The problem is that the 
differences in the means of the groups is not a valid concept when the age 
slopes are different

  1.
Thanks in advance
Rodrigo


De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 en nombre de Douglas Greve 

Enviado: martes, 29 de noviembre de 2016 07:33:47 p. m.
Para: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] Demeaning variables


It comes down to the contrast you care about. If you want to look at the 
difference in mean thickness between the groups regressing out the effect of 
age, then demeaning can make a big difference. If this is what you want, then 
you need to do the analysis in two stages. First run with DODS and see if there 
are any places where there is an interaction between age and group; demeaning 
is unimportant for this contrast. If there is not a difference, then reanalyze 
using DOSS (in which case demeaning is also unimportant). You cannot do DOSS in 
QDEC.


On 11/29/16 6:23 PM, Rodrigo Gonzalez Huerta wrote:

 Hi Doug,


I mean that when I run QDEC selecting gender and diagnosis as fixed factors, 
age as nuisance factor, and display the results, I obtain totally different 
significant statistical regions (different statistical maps) when ages are 
demeaned ((demeaned age = age of each subject – the mean of all subjects 
(grandmean)) than the case when ages aren't demeaned. Therefore, when I run the 
monte carlo simulation, when I demean the age variable I don’t get any 
clusters, but when age is not demeaned I obtain some clusters of considerable 
size. The contrast I used in mri_glmfit is:



0.5 -0.5 0.5 -0.5 0 0 0 0 ("is there a difference between patient and control 
regressing out the effects of gender and age?")



In QDEC it seems to correspond to the output 'Does the average thickness 
accounting for gender differ between patient and control? (age as nuisance 
variable)’ because the statistical maps look the same.



>From what I understand, this difference in the results when age variable is 
>demeaned is something I should expect when doing a DODS analysis. My main 
>doubt would be if it was necessary to demean the age variable and enter it as 
>a nuisance factor based on the characteristics of my population and the 
>analysis I want to perform. I tried to focus my questions in that direction. 
>I’m very sorry if I am not giving myself to understand. Thanks!


Rodrigo


De: 

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html). 
He mentioned that obtaining a new license could solve the issue. It did, 
so my problem is resolved.

Best,

Vincent




Dear Anastasia,

I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is
because I only have this issue with the mri_convert that is bundled with
the TRACULA update (see my first post). The original mri_convert bundled
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
  -f,  --frame frameno
  keep only 0-based frame number

Frame options of the updated mri_convert
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
  -f,  --frame frameno [...]
  keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Matt Glasser]

Hi Antonin,

In our experience with FreeSurfer 5.3 we were getting very consistent
results.  We are going to try some of this locally and work with the
FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+.

Thanks for testing this,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Wednesday, November 30, 2016 at 3:31 PM
To:  
Subject:  Re: [Freesurfer] freesufer v6 beta - T2 pial refinement
performance and nsigma_below setting

Dear experts,

given sub-optimal results of my surfaces I referred to in my previous post,
I have tested several different settings and input data preparation to
obtain optimal pial surfaces in my modified HCP pipeline. I tested all
variants in 5 representative subjects.

My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm
option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and
FreeSurferHiResPial.sh where effectively no up and downsampling is done
since all steps are done in original 0.7 mm3 resolution).

I have played with input data and parameters of 2nd pass mris_make_surfaces
-T2pial in FreeSurferHiResPial.sh
Since FreeSurferHiResPial.sh does not use aseg-informed and white
surface-informed normalization and brain masking of T2 (which is default in
recon-all), I also tested performance of this option (using commands
borrowed from recon-all -T2pial). Since -nsigma_below 3 (default in
FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of
mris_make_surfaces cuts out some portions of gray matter in my data (in
contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3
suffices!), I increased -nsigma_below to 5 (which is default value used in
recon-all -T2pial).

My tested versions were following:
For modified full hires HCP pipeline with FreeSurfer V6beta:
1. -nsigma_below 3 (original FreeSurferHiResPial.sh)
2. -nsigma_below 5 
3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz
4. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize)
5. -nsigma_below 5 with aseg-informed normalization of T2 (using
mri_normalize) and masking of T2 by brainmask.mgz

And, as Matt suggested, I also tried:
6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from
standard recon-all I used as ?h.white input the output of
FreeSurferHiResWhite.sh , but I think it should not matter in this context).

My observations are following:

It is definitely needed to increase -nsigma_below from 3 due to significant
cut out of portions of gray matter in some regions, in some subjects these
regions are very large.

Increase nsigma_below to 5 prevents cutting out of gray matter, however it
leads to leak of surfaces to cerebellum (as I showed in my previous post)
for all my versions (to varying extent). I am not sure how much significant
the extend of error is, looking subjective it seems significant, but
accounting the fact that the data is of high resolution, the maximal error
would be approx. 2 mm.

-nsigma_below 5 with aseg-informed normalization does not work well in some
areas and results in cutting out gray matter in some regions (but not to
such great extend as in nsigma_below 3)

FreeSurfer V6beta tends in some (not very large) areas to cut out gray
matter. On the other hand, in some areas and in some subjects it produces
largest leak of surfaces to dura and cerebellum from all my tested versions.

mri_normalize of T2 has in some regions  sub-optimal performance on pial
surface estimation and actually performs worse than global (no aseg-informed
and no white surface-informed) normalization ( especially at temporal poles,
but also in some areas at convexity).

I have indecisive results with masking. In some subjects it had almost no
effect, in one subject it definitely improved the leak to dura, but in some
subjects the results were quite opposite. I am not sure why the masking
should matter since the mask is larger than the regions where the surfaces
are extending, but I am not very familiar with internals of
mris_make_surfaces (the masked T2 maybe after internal smoothing in
mris_make_surfaces can propagate the voxel values even to regions relevant
for surface estimation). Therefore I would tend to use the masking.

Overall best results (better than with V6beta recon-all) I obtained with
-nsigma_below 5 with global (no aseg-informed and white surface-informed)
normalization of T2 as it is done in FreeSurferHiResPial.sh.

My overall impresion: I was quite frustrated to observe, how much the
results are dependent on particular setting of the parameters and input
data. But maybe my expectations of accuracy of surfaces were unrealistically
high

Regards,

Antonin
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Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

[Knut J Bjuland]

Hi  Anastasia

If I want to use Tracula DTI files instead, which file do I choose: Is it 
FA_ditifit.nii?

Best

Knut Jørgen



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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

[Antonin Skoch]

Dear experts,

given sub-optimal results of my surfaces I referred to in my previous post, I 
have tested several different settings and input data preparation to obtain 
optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5 
representative subjects.

My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm 
option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and 
FreeSurferHiResPial.sh where effectively no up and downsampling is done since 
all steps are done in original 0.7 mm3 resolution).

I have played with input data and parameters of 2nd pass mris_make_surfaces 
-T2pial in FreeSurferHiResPial.sh
Since FreeSurferHiResPial.sh does not use aseg-informed and white 
surface-informed normalization and brain masking of T2 (which is default in 
recon-all), I also tested performance of this option (using commands borrowed 
from recon-all -T2pial). Since -nsigma_below 3 (default in 
FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of 
mris_make_surfaces cuts out some portions of gray matter in my data (in 
contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3 
suffices!), I increased -nsigma_below to 5 (which is default value used in 
recon-all -T2pial).

My tested versions were following:
For modified full hires HCP pipeline with FreeSurfer V6beta:
1. -nsigma_below 3 (original FreeSurferHiResPial.sh)
2. -nsigma_below 5 
3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz
4. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize)
5. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize) 
and masking of T2 by brainmask.mgz

And, as Matt suggested, I also tried:
6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from standard 
recon-all I used as ?h.white input the output of FreeSurferHiResWhite.sh , but 
I think it should not matter in this context).

My observations are following:

It is definitely needed to increase -nsigma_below from 3 due to significant cut 
out of portions of gray matter in some regions, in some subjects these regions 
are very large.

Increase nsigma_below to 5 prevents cutting out of gray matter, however it 
leads to leak of surfaces to cerebellum (as I showed in my previous post) for 
all my versions (to varying extent). I am not sure how much significant the 
extend of error is, looking subjective it seems significant, but accounting the 
fact that the data is of high resolution, the maximal error would be approx. 2 
mm.

-nsigma_below 5 with aseg-informed normalization does not work well in some 
areas and results in cutting out gray matter in some regions (but not to such 
great extend as in nsigma_below 3)

FreeSurfer V6beta tends in some (not very large) areas to cut out gray matter. 
On the other hand, in some areas and in some subjects it produces largest leak 
of surfaces to dura and cerebellum from all my tested versions. 

mri_normalize of T2 has in some regions  sub-optimal performance on pial 
surface estimation and actually performs worse than global (no aseg-informed 
and no white surface-informed) normalization ( especially at temporal poles, 
but also in some areas at convexity). 

I have indecisive results with masking. In some subjects it had almost no 
effect, in one subject it definitely improved the leak to dura, but in some 
subjects the results were quite opposite. I am not sure why the masking should 
matter since the mask is larger than the regions where the surfaces are 
extending, but I am not very familiar with internals of mris_make_surfaces (the 
masked T2 maybe after internal smoothing in mris_make_surfaces can propagate 
the voxel values even to regions relevant for surface estimation). Therefore I 
would tend to use the masking.

Overall best results (better than with V6beta recon-all) I obtained with 
-nsigma_below 5 with global (no aseg-informed and white surface-informed) 
normalization of T2 as it is done in FreeSurferHiResPial.sh.

My overall impresion: I was quite frustrated to observe, how much the results 
are dependent on particular setting of the parameters and input data. But maybe 
my expectations of accuracy of surfaces were unrealistically high

Regards,

Antonin___
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Re: [Freesurfer] TR : recon-all exited with ERRORS in Talairach

[Z K]

Hello Jean-Simon,

If indeed you are running the same subject on the same machine, then the 
reason its failing has to be because of an update to perl. It's possible 
your Linux update also updated the version of perl, even if only a minor 
verion update, and this is what created the issue. You have two 
solutions to using for using freesurfer at this point...

1) Update your version of freesurfer to the v6-beta release which fixes 
the issue (the official v6 should be released in just a matter of 1-2).

2) Install perlbrew and use that to install perl version 5.20.3

  $> sudo apt-get install perlbrew
  $> perlbrew install perl-5.20.3

You then must change the first line of any mni script that fails (their
should only be a few) to point to the perl v5.20 instead of the default.
So for example, the first line of $FREESURFER_HOME/mni/bin/nu_correct
should be changed from:

  #!/usr/bin/perl -w
to:
  #!~/perl5/perlbrew/perls/perl-5.20.3/bin/perl -w

You may need to do this with a couple of the MNI scripts. I know this is
not an ideal solution but it is the only way I know of to get
freesurfer5.3 working on platforms with perl 5.22

-Zeke




On 11/30/2016 02:51 PM, jean-simon.bouche...@ens.etsmtl.ca wrote:
> Hi Freesurfer Developpers,
>
> I'm trying to ''recon-all'' my MRI and I got an error in Talairach parts of 
> the process. This is strange because I was able to complete the process 
> entirely few weeks ago ...
>
> Here are the recon-all log files for the same subjects (the good one (few 
> weeks ago) and the new one that I got now with ERROR).
> I've compared the 2 files and the only thing that is different is my 
> platformversion (this is the linux version, right?). It has increased from 
> 4.4.0.38 to 4.4.0.47.
>
> The only things that I have changed since the first time that I was able to 
> perform the freesurfer process are:
> - Update on Linux
> - Installation of a new hard drive. Note here that I've tried to bypass (not 
> using) the hard drive in my process.
>
> I've tried a lot of thing and one things that seem to be my problem is the 
> Version of Perl (5.22.1) with my version of Freesurfer (5.3.0).
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048807.html)
> Strangely, I haven't upgraded any of theses since the first time that I was 
> able to run Freesurfer. Moreover, I don't have the access to change the 
> version of perl (yes I've tried to change it for version 5.16)
>
> Do you have any idea what I'm doing wrong?
>
> Thanks a lot!
>
> Jean-Simon Boucher
> B. Ing. Électrique (ÉTS)
>
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer.
>
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Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I have checked the image and it looks good. I don't think the image is 
the problem, especially considering that my issue is also popping up 
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz 
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is 
because I only have this issue with the mri_convert that is bundled with 
the TRACULA update (see my first post). The original mri_convert bundled 
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert 
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
 -f,  --frame frameno
 keep only 0-based frame number

Frame options of the updated mri_convert 
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
 -f,  --frame frameno [...]
 keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert 
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA 
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent
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Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Yendiki, Anastasia]

Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but 
probably something about the format of your input nifti volume. How did you 
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans 
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

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dispose of the e-mail.

[Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early 
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

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Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

[Douglas N Greve]

Doug, can you do me a favor and check to see if this modified version of 
recon-all works on your data?

https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all



On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension 
> gives it problems?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 5:01 PM, Douglas N Greve 
> >
>  wrote:
>
>> It is not recognizing that the input is a dicom file. Is 4355-0005-1
>> a dicom file? Or is it a folder?
>>
>>
>> On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
>>> Here is the command/output with the -debug flag:
>>>
>>> recon-all -debug -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> -s 1039_test
>>> set echo = 1 ;
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 6 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 5 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > /dev/null
>>> popd
>>> set InputVol = "$InVolDir/$InVolBase" ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InputList = ( $InputList "$InputVol" ) ;
>>> set InputList = (
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> )
>>> set DoConvertInput = 1 ;
>>> set DoConvertInput = 1
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 4 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 3 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > 

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

[Douglas N Greve]

Actually, it is the lack of a dot (".") in the file name. This is a 
short-coming of recon-all. I'm really surprised that it took this long 
to manifest itself. The short-term fix is to convert the files to mgz, 
then pass the mgz files to recon-all.


On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension 
> gives it problems?
>
> Thanks,
>
> Doug
>
> Douglas Merkitch
> Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853 
> Fax: (312) 563-4660 
> Email: douglas_merki...@rush.edu 
>
>
>
>
>
> On Nov 29, 2016, at 5:01 PM, Douglas N Greve 
> >
>  wrote:
>
>> It is not recognizing that the input is a dicom file. Is 4355-0005-1
>> a dicom file? Or is it a folder?
>>
>>
>> On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
>>> Here is the command/output with the -debug flag:
>>>
>>> recon-all -debug -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> -i
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> -s 1039_test
>>> set echo = 1 ;
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 6 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 5 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE
>>> set InVolDir = `pwd` ;
>>> set InVolDir = `pwd`
>>> pwd
>>> popd > /dev/null
>>> popd
>>> set InputVol = "$InVolDir/$InVolBase" ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>> set InputList = ( $InputList "$InputVol" ) ;
>>> set InputList = (
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1
>>>  
>>>
>>> )
>>> set DoConvertInput = 1 ;
>>> set DoConvertInput = 1
>>> breaksw
>>> breaksw
>>> end
>>> end
>>> while ( $#argv != 0 )
>>> while ( 4 != 0 )
>>>
>>> set flag = $argv[1] ; shift ;
>>> set flag = -i
>>> shift
>>>
>>> switch ( $flag )
>>> switch ( -i )
>>> if ( $#argv < 1 ) goto arg1err ;
>>> if ( 3 < 1 ) goto arg1err
>>> set InputVol = "$argv[1]" ; shift ;
>>> set InputVol =
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> shift
>>> if ( ! -e "$InputVol" ) then
>>> if ( ! -e
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( -d "$InputVol" ) then
>>> if ( -d
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> if ( ! -r "$InputVol" ) then
>>> if ( ! -r
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>>  
>>>
>>> ) then
>>> set InVolDir = `dirname  "$InputVol"` ;
>>> set InVolDir = `dirname  "$InputVol"`
>>> dirname
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> set InVolBase = `basename "$InputVol"` ;
>>> set InVolBase = `basename "$InputVol"`
>>> basename
>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1
>>> pushd $InVolDir > /dev/null
>>> pushd
>>> 

Re: [Freesurfer] DTI Multi band sequence?

[Harms, Michael]

That would be yet another way.
For those that are curious, the field is “MosaicRefAcqTimes”.

cheers,
-MH
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 11/30/16, 11:16 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of dgw"  wrote:

I can't remember the tag numbers, but I believe the time of slice
acquisition is in the dicom. You should be able to just pull that
field on one volume and compare the field for all slices and see if
any of them have the same time.

hth
d

On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja  wrote:
> Hi,
>
> I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
> whether the DTI data (in DICOM format) I have is multi-band sequence?
>
> I used dicominfo in MATLAB but couldn't find any information related to
> multi-band in the dicom header.
>
> Any help would be really appreciated.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] DTI Multi band sequence?

[dgw]

I can't remember the tag numbers, but I believe the time of slice
acquisition is in the dicom. You should be able to just pull that
field on one volume and compare the field for all slices and see if
any of them have the same time.

hth
d

On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja  wrote:
> Hi,
>
> I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
> whether the DTI data (in DICOM format) I have is multi-band sequence?
>
> I used dicominfo in MATLAB but couldn't find any information related to
> multi-band in the dicom header.
>
> Any help would be really appreciated.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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Re: [Freesurfer] DTI Multi band sequence?

[Harms, Michael]

Hi Martin,
I’ve addressed this in your query to the FSL list.  Please see my response 
there.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of Martin Juneja >
Reply-To: Freesurfer support list 
>
Date: Wednesday, November 30, 2016 at 11:10 AM
To: Freesurfer support list 
>
Subject: [Freesurfer] DTI Multi band sequence?

Hi,

I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine 
whether the DTI data (in DICOM format) I have is multi-band sequence?

I used dicominfo in MATLAB but couldn't find any information related to 
multi-band in the dicom header.

Any help would be really appreciated.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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[Freesurfer] DTI Multi band sequence?

[Martin Juneja]

Hi,

I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
whether the DTI data (in DICOM format) I have is multi-band sequence?

I used dicominfo in MATLAB but couldn't find any information related to
multi-band in the dicom header.

Any help would be really appreciated.
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Re: [Freesurfer] longHippoSubfields

[Christian Krog Tamnes]

We will get the beta for now then.

Thanks Eugenio!



regards,

Christian








From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: 30 November 2016 15:46
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSubfields

Hi Christian,
I believe you were unlucky enough to download the dev version during the days 
that this module was broken.
I would strongly suggest that you either download the beta version of 6.0 or 
wait until the official release of this version, which should be happening soon.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Nov 2016, at 14:26, Christian Krog Tamnes 
> wrote:

Dear Juan and FreeSurfer team,



We are trying to test out the longitudinal hippocampus subfield segmentation 
pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We 
have done the standard processing in v5.3 and have the following dev version: 
freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic 
question, but do we simply need a later dev build?



Best regards,
Christian
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Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

[Yendiki, Anastasia]

Hi Knut Jørgen - The aparc+aseg doesn't contain the wm-* labels, only the 
cortical labels from the aparc (in the 1000's and 2000's) and subcortical 
labels from the aseg. The wm labels (in the 3000's and 4000's) are in the 
wmparc only.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Knut J Bjuland 
[knutjor...@outlook.com]
Sent: Wednesday, November 30, 2016 5:35 AM
To: Freesurfer support list
Subject: [Freesurfer] obtain fa FA data from the white matter ROIs in 
WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi,

I would like to to obtain FA data from the white matter ROIs in 
WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a 
DWI file, either produced by  dt_recon (or perhaps better - from Tracula) and 
an anatomy file in atlas space and then use WMParcStatsLUT.txt or 
FreeSurferColorLUT.txt  (not sure which) to obtain the wm ROIs containing FA 
data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats 
to retrieve FA data from the white matter ROIs.

I have done this:
# Register DTI file to individual anatomy space
1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon

# Register fa.nii to wmparc.mgz and aparc+aseg.mgz
2)
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/wmparc.mgz   --inv --interp nearest --o 1/mri/aseg2DTI.mgz
   --no-save-reg
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz 
--no-save-reg

3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean 
= 0.04 (which is a little low for FA values):
mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

But for aparc+aseg, it doesn't produce any data:
mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

output:
Found   1 segmentations
Computing statistics for each segmentation
  0   3014  wm-lh-medialorbitofrontal   0   0.000

Reporting on   0 segmentations
mri_segstats done



Questions:
1) Am I right to use FreeSurferColorLUT.txt   and not WMParcStatsLUT.txt?
2) In order to get FA data from the wm regions corresponding to cortical ROIs, 
should I use the FA registrated to wmparc.mgz  or aparc+aseg.mgz?
3) If I want to use Tracula DTI files instead, which file do I choose: Is it 
FA_ditifit.nii?


sincerely yours,

Knut Jørgen Bjuland PhD


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Re: [Freesurfer] longHippoSubfields

[Iglesias Gonzalez, Eugenio]

Hi Christian,
I believe you were unlucky enough to download the dev version during the days 
that this module was broken.
I would strongly suggest that you either download the beta version of 6.0 or 
wait until the official release of this version, which should be happening soon.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Nov 2016, at 14:26, Christian Krog Tamnes 
> wrote:

Dear Juan and FreeSurfer team,



We are trying to test out the longitudinal hippocampus subfield segmentation 
pipeline, but can’t seem to run/find the script (longHippoSubfieldsT1.sh). We 
have done the standard processing in v5.3 and have the following dev version: 
freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic 
question, but do we simply need a later dev build?



Best regards,
Christian
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[Freesurfer] longHippoSubfields

[Christian Krog Tamnes]

Dear Juan and FreeSurfer team,



We are trying to test out the longitudinal hippocampus subfield segmentation 
pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We 
have done the standard processing in v5.3 and have the following dev version: 
freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic 
question, but do we simply need a later dev build?



Best regards,

Christian
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

[Knut J Bjuland]

Hi, 

I would like to to obtain FA data from the white matter ROIs in 
WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a 
DWI file, either produced by  dt_recon (or perhaps better - from Tracula) and 
an anatomy file in atlas space and then use WMParcStatsLUT.txt or 
FreeSurferColorLUT.txt  (not sure which) to obtain the wm ROIs containing FA 
data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats 
to retrieve FA data from the white matter ROIs. 

I have done this: 
# Register DTI file to individual anatomy space
1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon

# Register fa.nii to wmparc.mgz and aparc+aseg.mgz 
2) 
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/wmparc.mgz   --inv --interp nearest --o 1/mri/aseg2DTI.mgz
   --no-save-reg
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz 
--no-save-reg

3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean 
= 0.04 (which is a little low for FA values): 
mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

But for aparc+aseg, it doesn't produce any data:
mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

output:
Found   1 segmentations
Computing statistics for each segmentation
  0   3014  wm-lh-medialorbitofrontal   0   0.000

Reporting on   0 segmentations
mri_segstats done



Questions: 
1) Am I right to use FreeSurferColorLUT.txt   and not WMParcStatsLUT.txt? 
2) In order to get FA data from the wm regions corresponding to cortical ROIs, 
should I use the FA registrated to wmparc.mgz  or aparc+aseg.mgz?
3) If I want to use Tracula DTI files instead, which file do I choose: Is it 
FA_ditifit.nii?


sincerely yours,

Knut Jørgen Bjuland PhD


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