[Freesurfer] Qdec Generate Stats Data Table Error

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello All,

My table.dat file loaded fine. However, I came across the following error when 
I was running the Qdec generate stats data table. If you can let me know what I 
can do to fix the following error I would greatly appreciate it.

Uncaught exception: command failed: asegstats2table --common-segs --meas volume 
--tablefile 
/local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat 
--statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 
CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 
CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 
CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 
CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 
CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 
PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 
PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 
PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440


SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects

Parsing the .stats files

ERROR: The stats file 
/local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or 
is too small to be a valid statsfile

Use --skip flag to automatically skip bad stats files


Thanks,

Gaurang


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Re: [Freesurfer] V6.0 Hippocampal subfield segmentation

[Iglesias, Eugenio]

Dear Xiaowei,
That beta version was taken down because it had several problems. I would 
recommend that you wait until the next beta comes out (hopefully in 2 weeks or 
so), or that you download the development version (in that case, I’d do it next 
week because we currently fixing an error I accidentally introduced in the 
hippocampal subfield module).
Cheers,
Eugenio

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


On 27 Jul 2016, at 20:23, Zhuang, Xiaowei 
mailto:zhua...@ccf.org>> wrote:

Hi everyone,

I am running the new hippocampal subfield segmentation with a V6.0 beta version 
released last year on 20150724.

There is only 1 subject (out of about 40 total) exit with an ERROR during 
segmentation with T1 input. All others subjects ran through the hippocampal 
segmentation and gives me reasonable results.

And the same T1 image ran through the V5.3 old hippocampal segmentation so I 
believe there is nothing wrong with image itself.

I am wondering is this a bug in the beta version of V6.0 I am having? And I 
have attached the two ERROR log files. Any response will be appreciated.

Thanks,
Xiaowei.





Xiaowei Zhuang   |  Research Engineer  |  Lou Ruvo Center for Brain Health
 Cleveland Clinic  |  888 W Bonneville Ave.   |  Las Vegas, NV 89106  | (702) 
685-6051




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Re: [Freesurfer] Recent error in the dev version

[Iglesias, Eugenio]

Hi Daniel,
the problems was that I accidentally compiled the module against dynamic rather 
than static libraries. The code will be fixed in the development version very 
soon.
Also, I introduced some changes in the code so that it can handle high 
resolution T1s, but the behaviour on standard resolution T1 data hasn’t changed.
I hope this helps.
Cheers,
Eugenio 

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


> On 27 Jul 2016, at 20:49, Liu, Daniel  wrote:
> 
> Hi,
> 
> I'm an undergraduate learning about/working with freesurfer as part of my 
> summer research project.  In early-mid June I downloaded the dev version of 
> Freesurfer to use on my mac.  When I ran it at that time, I had no problem.  
> Recently I started working on a cluster computer (linux) and got the same 
> problem outlined in this exchange:
> 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html.
> 
> 
> I was wondering if I could get an update on this and possibly an explanation 
> as to what the problem was.  I was told that the dev version on the cluster 
> was updated today (with the fixed version as mentioned in the email) but I 
> still got that message after running the program.
> 
> 
> Also, were there any major changes to the program that I should be aware 
> about in terms affecting data analysis of the MRI patient data for the 
> hippocampus subfields tool?
> 
> 
> If you could let me know, it would be appreciated.
> 
> 
> Thanks,
> 
> 
> Daniel
> 
> 
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[Freesurfer] Recent error in the dev version

[Liu, Daniel]

Hi,

I'm an undergraduate learning about/working with freesurfer as part of my 
summer research project.  In early-mid June I downloaded the dev version of 
Freesurfer to use on my mac.  When I ran it at that time, I had no problem.  
Recently I started working on a cluster computer (linux) and got the same 
problem outlined in this exchange:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html.


I was wondering if I could get an update on this and possibly an explanation as 
to what the problem was.  I was told that the dev version on the cluster was 
updated today (with the fixed version as mentioned in the email) but I still 
got that message after running the program.


Also, were there any major changes to the program that I should be aware about 
in terms affecting data analysis of the MRI patient data for the hippocampus 
subfields tool?


If you could let me know, it would be appreciated.


Thanks,


Daniel


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[Freesurfer] Assessing local correlations across 2 modalities

[Elijah Mak]

Dear Freesurfer Community,

I am currently trying to investigate the local correlations across 2
modalities (i.e. Tau-PET and cortical thinning). I understand that this
sort of questions has been conventionally addressed using the Biological
Parametric Mapping (BPM) toolbox in MATLAB.

Is there a way in Freesurfer to properly address this?

My PET data have already been registered and projected to the surfaces for
each individual.

Thanks a lot.

Best Wishes,
Elijah

-- 

Elijah Mak

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] V6.0 Hippocampal subfield segmentation

[Zhuang, Xiaowei]

Hi everyone,

I am running the new hippocampal subfield segmentation with a V6.0 beta version 
released last year on 20150724.

There is only 1 subject (out of about 40 total) exit with an ERROR during 
segmentation with T1 input. All others subjects ran through the hippocampal 
segmentation and gives me reasonable results.

And the same T1 image ran through the V5.3 old hippocampal segmentation so I 
believe there is nothing wrong with image itself.

I am wondering is this a bug in the beta version of V6.0 I am having? And I 
have attached the two ERROR log files. Any response will be appreciated.

Thanks,
Xiaowei.


[Cleveland Clinic logo]


Xiaowei Zhuang   |  Research Engineer  |  Lou Ruvo Center for Brain Health
 Cleveland Clinic  |  888 W Bonneville Ave.   |  Las Vegas, NV 89106  | (702) 
685-6051




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Thank you.


hippocampal-subfields-T1.log
Description: hippocampal-subfields-T1.log


recon-all.error
Description: recon-all.error
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Re: [Freesurfer] ROIs defined in MNI space and vol2surf

[Trisanna Sprung-Much]

Hey there

I think you just need to use "--regmethod subject" instead of specifying a
registration .dat file. I had similar troubles a few months ago as my
labels were made on the volume and I simply wanted to overlay them onto
their surfaces in Freesurfer and didn't want any transformation to be made.

Best wishes

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jul 27, 2016 at 12:07 PM, Funk, Quentin 
wrote:

> All,
>
> I have a question regarding the required registration file in mri_vol2surf.
>
> I have some spherical ROI's in MNI space produced via 3dUndump--they're
> volume files that show up in the correct places when loaded in with an
> MNI standard subject such as fsaverage.
>
> I also have some patients scans. I'd really like to compute cortical
> thickness for these ROI's on my patient scans, so I attempt to follow
> the instructions at (
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ),
> but these instructions assume that the ROI is in the native space--which
> produces no problems until the step :
>
> cd $SUBJECTS_DIR/fsaverage/surf
> mri_vol2surf \
>--mov /path/to/ROI5.nii \
>--reg TT_avg152T1_to_fsaverage.dat \
>--projdist-max 0 1 0.1 \
>--interp nearest \
>--hemi lh \
>--out lh.fsaverage.ROI5.mgh \
>--reshape
>
> My question is then three parts:
>
> (1) Why does vol2surf require a registration file? Shouldn't it be
> possible to do it as a straight conversion of data types if I know that
> my surface is registered to the file that I want? Perhaps naive, my
> first intuition was to construct a TT.dat that was the identity matrix,
> but this fails, with the response listed in (2).
>
> (2) How can I do this without shifting my data? If I follow the
> instructions, when the surface is overlayed on fsaverage's lh.pial, the
> entire surface is included in the overlay.
>
> (3) What exactly do the numbers mean in the registration file TT.dat (as
> in the instructions on the website)? The 4x4 matrix is clear, and the
> first two numbers appear to have something to do with Voxel resolution,
> but I'm unable to find documentation that explains the notation in the
> output.
>
> Any help anyone can offer would be tremendously appreciated.
>
> -qf
>
> Houston Methodist. Leading Medicine.
>
> Ranked by U.S.News & World Report as one of America's "Best Hospitals" in
> 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work
> For®" list 10 years in a row. Designated as a Magnet hospital for
> excellence in nursing. Visit us at houstonmethodist.org. Follow us at
> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
>
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[Freesurfer] ROIs defined in MNI space and vol2surf

[Funk, Quentin]

All,

I have a question regarding the required registration file in mri_vol2surf.

I have some spherical ROI's in MNI space produced via 3dUndump--they're 
volume files that show up in the correct places when loaded in with an 
MNI standard subject such as fsaverage.

I also have some patients scans. I'd really like to compute cortical 
thickness for these ROI's on my patient scans, so I attempt to follow 
the instructions at ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ), 
but these instructions assume that the ROI is in the native space--which 
produces no problems until the step :

cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
   --mov /path/to/ROI5.nii \
   --reg TT_avg152T1_to_fsaverage.dat \
   --projdist-max 0 1 0.1 \
   --interp nearest \
   --hemi lh \
   --out lh.fsaverage.ROI5.mgh \
   --reshape

My question is then three parts:

(1) Why does vol2surf require a registration file? Shouldn't it be 
possible to do it as a straight conversion of data types if I know that 
my surface is registered to the file that I want? Perhaps naive, my 
first intuition was to construct a TT.dat that was the identity matrix, 
but this fails, with the response listed in (2).

(2) How can I do this without shifting my data? If I follow the 
instructions, when the surface is overlayed on fsaverage's lh.pial, the 
entire surface is included in the overlay.

(3) What exactly do the numbers mean in the registration file TT.dat (as 
in the instructions on the website)? The 4x4 matrix is clear, and the 
first two numbers appear to have something to do with Voxel resolution, 
but I'm unable to find documentation that explains the notation in the 
output.

Any help anyone can offer would be tremendously appreciated.

-qf

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Re: [Freesurfer] TRACULA: 20% default threshold

[Anastasia Yendiki]

Yes, same thing!

On Wed, 27 Jul 2016, Harms, Michael wrote:



Thanks for clarifying.  Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?

thx,
--
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 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Dillan - Thank you for your support!

Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.

Best,

a.y

On Tue, 26 Jul 2016, Newbold, Dillan wrote:


Hi everyone,

I’m having a little trouble understanding the exact meaning of the 20%
default threshold used in the freeview -tv option and dmri_pathstats
--pthr. I’ve seen multiple threads where Anastasia said that it is 20% of
the maximum value in the probability distribution—which corresponds to
the maximum number of sample paths intersecting a single voxel—but the
default thresholds I’ve seen set by the -tv option are generally lower
than that. For example, I have one subject in whom the right CST has a
maximum value in its path.pd.nii.gz file of 300. I would expect based on
what I’ve read in the mail archives that the threshold would be set at
60, but when I open the merged file with the -tv option the default
threshold for the right CST is 35.

My current best guess is that the default threshold is set to produce a
volume that has a probability sum equal to 20% of the sum of the
pre-threshold volume. (That is, the sum of intensities of all voxels in
the path.pd.nii.gz file should be 5 times the sum of the voxels above the
default threshold.) Is that accurate?

Thanks for all you’ve done to develop this tool. It’s brilliant and I
want to understand as much of it as I can.

-Dillan

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Re: [Freesurfer] TRACULA fornix tractography

[Anastasia Yendiki]

Hopefully soon, as several people have asked for it, but I don't have a 
concrete date unfortunately.

On Wed, 27 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
>
> Thank you that is great! Do you know yet when it will be available?
>
> Best wishes,
>
> Barbara
>
>
> On 27/07/2016 06:25, Anastasia Yendiki wrote:
>> Hi Barbara - We're working on a new atlas for TRACULA that will include
>> the fornix. We've already done the manual labeling for it.
>>
>> Best,
>>
>> a.y
>>
>> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>>
>>> Dear Anastasia,
>>>
>>> As we are analyzing DTI data acquired in patients with epilepsy we are
>>> especially interested in the fornix.
>>> I've come across the mri_cc -f option for fornix segmentation (native space)
>>> but I've also read that manual tracing/labeling of the tracts would be
>>> needed in the 33 controls for TRACULA (training set - trctrain).
>>> In Wakana et al. 2011 I see that the fornix was not included due to low
>>> reproducibility and it further states:
>>>
>>> "the reason for the poor reproducibility is most likely due to not enough
>>> spatial resolution with respect to the diameter"
>>>
>>> I wonder if you could please guide us in how to best add this tract to
>>> TRACULA so that it would be consistent in the methods compared with the
>>> other tract ROI definitions or perhaps state what were the difficulties in
>>> adding this particular tract to TRACULA.
>>>
>>> Thank you very much,
>>> Best wishes,
>>> Barbara
>>>
>>>
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>> properly
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>
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[Freesurfer] R: R: problems by running longitudinal mass univariate analysis

[Valsasina Paola]

Dear Martin

thank you for your answer. Yes, it was a collinearity problem in the design 
matrix. I modified it and now everything works fine
Best
paola



Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Martin Reuter
Inviato: 27 July 2016 17:16
A: Freesurfer support list
Oggetto: Re: [Freesurfer] R: problems by running longitudinal mass univariate 
analysis

Hi Paola,

there is probably a problem with the design matrix. What exactly are the 
columns of M ?

Also how many subjects (and time points) do you have?

I am not sure, but I think you can open a thickness stack on top of the 
corresponding surface (from fsaverag) in freeview. It will think it is a time 
course, but that is OK. Not sure how to switch between the thicknesses, but 
there is a way to click a vertex and see the time course (all the thickness 
values at that location).  Also Qdec may do that.

Best, Martin
On 07/20/2016 10:35 AM, Valsasina Paola wrote:
Dear Martin

to follow-up mu previous question, I was finally able to run the 
lme_mass_fit_vw script till the end. Unfortunately, it came out that converge 
of the algorithm was failed in 99% of the locations.
I have only one study group (with a variable number of follow-up , and I used 
as design matrix exactly the same proposed in the online guide:
X=[ones(length(M),1) M M(:,1).*M(:,2)]

so, I don’t see any specific region of failure associated with the design 
matrix

Therefore, I suppose that this is due to the fact that input images are wrong 
(empty or with some problems?).
How can I investigate further the correctness of my input data? The 
longitudinal pipeline was performed correctly, and mris_preproc command to 
generate the mass univariate file seems to work without errors. Can I 
eventually load somewhere my image file (i.e., the concatenated 
lh.thickness.mgh including all scans), so that someone chan check that input 
images for lme estimation are OK?
Thank you so much in advance
Kind regards
Paola


Da: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Martin Reuter
Inviato: 14 July 2016 12:12
A: Freesurfer support list
Oggetto: Re: [Freesurfer] problems by running longitudinal mass univariate 
analysis


Hi Paola,

1 . It really takes a long time, though I think you probably are missing the 
parallel toolbox, and running this sequentially will be really slow.

2. You need to wait till the end and look at the percent of places where it did 
not converge. It is normal that it does not converge in some places. Also make 
sure the design matrix is not (close to) singular, which can happen if you have 
nearly collinear columns.

Best Martin
On Jul 14, 2016 10:43 AM, Valsasina Paola 
 wrote:

Dear FS experts



I am trying to run the commands for performing the longitudinal mixed effect 
statistics with the LME Matlab toolbox.

I am following the instructions on the web page; however, I have two questions:



1) when I run the command lme_mass_fit_vw, the script is running for a very 
long time, after 3 hours the estimation was just at 10% (unfortunately, my 
laptop is equipped with Windows and is not particularly powerful). I had to 
stop the script at that point; before restarting it again I would like to be 
sure: is this behavior normal?  Is it correct that lme_mass_fit_vw is running 
for such a long time?



2) when the script was running, there were several warnings on the Matlab 
screen, saying that the algorithm was not converging (at most of locations). Is 
it also normal? How can I check the correctness of my input image? When I open 
with freeview the “lh.thickness_sm10.mgh” volume, I just see a black screen 
with valid timeseries values in the minority of voxels (I imagine that these 
timeseries are concatenated thickness values of my study subjects). Is there 
another way to better visualize and check a concatenated 4d mgh file? Failure 
of convergence is referring to empty/zero voxels of this image?



Thank you for any advice on these two topics

Kind regards

Paola






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Re: [Freesurfer] R: problems by running longitudinal mass univariate analysis

[Martin Reuter]

Hi Paola,

there is probably a problem with the design matrix. What exactly are the 
columns of M ?


Also how many subjects (and time points) do you have?

I am not sure, but I think you can open a thickness stack on top of the 
corresponding surface (from fsaverag) in freeview. It will think it is a 
time course, but that is OK. Not sure how to switch between the 
thicknesses, but there is a way to click a vertex and see the time 
course (all the thickness values at that location).  Also Qdec may do that.


Best, Martin

On 07/20/2016 10:35 AM, Valsasina Paola wrote:


Dear Martin

to follow-up mu previous question, I was finally able to run the 
lme_mass_fit_vw script till the end. Unfortunately, it came out that 
converge of the algorithm was failed in 99% of the locations.


I have only one study group (with a variable number of follow-up , and 
I used as design matrix exactly the same proposed in the online guide:


X=[ones(length(M),1) M M(:,1).*M(:,2)]

so, I don’t see any specific region of failure associated with the 
design matrix


Therefore, I suppose that this is due to the fact that input images 
are wrong (empty or with some problems?).


How can I investigate further the correctness of my input data? The 
longitudinal pipeline was performed correctly, and mris_preproc 
command to generate the mass univariate file seems to work without 
errors. Can I eventually load somewhere my image file (i.e., the 
concatenated lh.thickness.mgh including all scans), so that someone 
chan check that input images for lme estimation are OK?


Thank you so much in advance

Kind regards

Paola

*Da:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *Per conto di *Martin 
Reuter

*Inviato:* 14 July 2016 12:12
*A:* Freesurfer support list
*Oggetto:* Re: [Freesurfer] problems by running longitudinal mass 
univariate analysis


Hi Paola,

1 . It really takes a long time, though I think you probably are 
missing the parallel toolbox, and running this sequentially will be 
really slow.


2. You need to wait till the end and look at the percent of places 
where it did not converge. It is normal that it does not converge in 
some places. Also make sure the design matrix is not (close to) 
singular, which can happen if you have nearly collinear columns.


Best Martin

On Jul 14, 2016 10:43 AM, Valsasina Paola  wrote:

Dear FS experts

I am trying to run the commands for performing the longitudinal mixed 
effect statistics with the LME Matlab toolbox.


I am following the instructions on the web page; however, I have two 
questions:


1) when I run the command lme_mass_fit_vw, the script is running for a 
very long time, after 3 hours the estimation was just at 10% 
(unfortunately, my laptop is equipped with Windows and is not 
particularly powerful). I had to stop the script at that point; before 
restarting it again I would like to be sure: is this behavior normal? 
 Is it correct that lme_mass_fit_vw is running for such a long time?


2) when the script was running, there were several warnings on the 
Matlab screen, saying that the algorithm was not converging (at most 
of locations). Is it also normal? How can I check the correctness of 
my input image? When I open with freeview the 
“lh.thickness_sm10.mgh� volume, I just see a black screen with 
valid timeseries values in the minority of voxels (I imagine that 
these timeseries are concatenated thickness values of my study 
subjects). Is there another way to better visualize and check a 
concatenated 4d mgh file? Failure of convergence is referring to 
empty/zero voxels of this image?


Thank you for any advice on these two topics

Kind regards

Paola

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riquadro RICERCA SANITARIA. Non c’è cura, senza ricerca. Non c’è 
ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org


Immagine rimossa dal mittente.



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  IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO

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centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel 
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ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org




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Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos C

Re: [Freesurfer] error during longitudinal -long stream

[Martin Reuter]

Hi Jinsong,

maybe not everything was copied? The link to fsaverage should be 
automatically created if it is missing. I often process cross in a 
different directory from base and long (and create symlinks to the cross 
subject dirs). It automatically creates fsaverage then.
Try to replicate your problem with a single subject that failed. First 
try to do everything on the same computer, then try to do what you did 
before (copying parts of it).


Best, Martin


On 07/20/2016 12:56 PM, Jinsong Tang wrote:

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem maybe we 
run cross on  a computer and then copy the results to another computer 
to run the cross and long. the "/fsaverage" is not copied. Does this 
matter？/


Best，

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Jinsong,

I have never seen this. Stable 5.3 is very stable and I doubt it
is a bug. How did you process base and cross sectionals? Also with
5.3 ?

I would recommend to process cross and base with 5.3, then re-run
the long and see if you can replicate this problem. Let me know
what happens.

Best, Martin


> On Jul 20, 2016, at 12:48 AM, Jinsong Tang
mailto:tangjinson...@gmail.com>> wrote:
>
> Hi all,
>
> I found an error during the longitudinal -long stream:
>
> recon-all -long P1001-2 P1001 -all
> ..
>
> FREESURFER_HOME /space/raid/fmri/freesurfer
> Actual FREESURFER_HOME /space/raid/fmri/freesurfer
> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7
17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
> ..
>
> mris_spherical_average -erode 1 -orig white -t 0.4 -o
P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average
lh.entorhinal_exvivo.label
>
> painting output onto subject P1001-2.long.P1001.
> processing subject lh.EC_average...
>

MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
could not open file
> eroding label 1 times before writing
> thresholding label stat at 0.400 before writing
> Not a directory
> mris_spherical_average: could not read surface file

/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
> Not a directory
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7
17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul  8
21:33:02 PDT 2016
>
>
> Please help me fix this error!
>
> Thanks and best regards,
>
> Jinsong
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] Error with selxavg3-sess

[Luft, Marissa]

I am running the following code: selxavg3-sess -s 1002a -analysis 
workmen.sm05.lh on data that was already preprocessed with preprocesses, 
mkanalysis-sess, and mkcontrast-sess.  I get the following error message:

outanadir = 
/Users/marissaluft/Documents/ROSE_Program/Jeff_Lab/Free_Surfer_Project/Project_Folder/1002a/bold/workmem.sm05.lh
Subscripted assignment dimension mismatch.

Error in fast_ldpar4 (line 97)
  par4(nthrow,1) = tonset;

Error in flac_customize (line 121)
[par partype] = fast_ldpar4(parpath);

Error in fast_selxavg3 (line 115)
flac = flac_customize(flac);


Thank you,
Marissa Luft
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Re: [Freesurfer] TRACULA: 20% default threshold

[Harms, Michael]

Thanks for clarifying.  Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?

thx,
--
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 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Dillan - Thank you for your support!

Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.

Best,

a.y

On Tue, 26 Jul 2016, Newbold, Dillan wrote:

> Hi everyone,
>
> I’m having a little trouble understanding the exact meaning of the 20%
>default threshold used in the freeview -tv option and dmri_pathstats
>--pthr. I’ve seen multiple threads where Anastasia said that it is 20% of
>the maximum value in the probability distribution—which corresponds to
>the maximum number of sample paths intersecting a single voxel—but the
>default thresholds I’ve seen set by the -tv option are generally lower
>than that. For example, I have one subject in whom the right CST has a
>maximum value in its path.pd.nii.gz file of 300. I would expect based on
>what I’ve read in the mail archives that the threshold would be set at
>60, but when I open the merged file with the -tv option the default
>threshold for the right CST is 35.
>
> My current best guess is that the default threshold is set to produce a
>volume that has a probability sum equal to 20% of the sum of the
>pre-threshold volume. (That is, the sum of intensities of all voxels in
>the path.pd.nii.gz file should be 5 times the sum of the voxels above the
>default threshold.) Is that accurate?
>
> Thanks for all you’ve done to develop this tool. It’s brilliant and I
>want to understand as much of it as I can.
>
> -Dillan
>
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Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Harms, Michael]

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

From the last post in that thread, it is unclear if the issue was ever
resolved.  Was it resolved off the list?

thanks,
-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 7/26/16, 11:22 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:


Hi Michael - Which build of freesurfer do you use? I can send you the new
version of dmri_paths so you can try it out.

Best,

a.y

On Wed, 20 Jul 2016, Harms, Michael wrote:

>
> Hi Anastasia,
>
> I was wondering what the resolution to this thread was:
>
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html
>
> It sounds like a new version of dmri_paths was deemed necessary to
> appropriately process single time points in the longitudinal TRACULA
>stream,
> but Janosch’s last post seemed to indicate that her issue wasn’t resolved
> even with the new build of dmri_paths that you generated.
>
> thanks,
> -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  63110 Email: mha...@wustl.edu
>
>
>
>
>
>__
>__
>
>
> 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] TRACULA fornix tractography

[Barbara Kreilkamp]

Dear Anastasia,

Thank you that is great! Do you know yet when it will be available?

Best wishes,

Barbara


On 27/07/2016 06:25, Anastasia Yendiki wrote:
> Hi Barbara - We're working on a new atlas for TRACULA that will include
> the fornix. We've already done the manual labeling for it.
>
> Best,
>
> a.y
>
> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Anastasia,
>>
>> As we are analyzing DTI data acquired in patients with epilepsy we are
>> especially interested in the fornix.
>> I've come across the mri_cc -f option for fornix segmentation (native space)
>> but I've also read that manual tracing/labeling of the tracts would be
>> needed in the 33 controls for TRACULA (training set - trctrain).
>> In Wakana et al. 2011 I see that the fornix was not included due to low
>> reproducibility and it further states:
>>
>> "the reason for the poor reproducibility is most likely due to not enough
>> spatial resolution with respect to the diameter"
>>
>> I wonder if you could please guide us in how to best add this tract to
>> TRACULA so that it would be consistent in the methods compared with the
>> other tract ROI definitions or perhaps state what were the difficulties in
>> adding this particular tract to TRACULA.
>>
>> Thank you very much,
>> Best wishes,
>> Barbara
>>
>>
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Re: [Freesurfer] flipping TRACULA tracts

[Barbara Kreilkamp]

Thank you Anastasia,

ah, yes, that might have been easier [I wonder though if I might have 
had some issues with different tract lengths etc.?]. I wanted to make 
sure that my coordinates relate to the tract, so I decided just to flip 
the x-coordinate, change the directory name and all the indication in 
the byvoxel.txt files pertaining to e.g. 'lh.unc' to 'rh.unc'. And I did 
all of this just for patients with right TLE. Then I ran trac-all stat 
-c ... and looked at 'lh' as those ipsilateral tracts and 'rh' as 
contralateral ones. Has worked as well.

All the best wishes,

Barbara


On 27/07/2016 06:32, Anastasia Yendiki wrote:
> Hi Barbara - Your hack sounds like the right idea. One option would be to
> switch the FA values between the pathstats.byvoxel.txt files in the lh.*
> and rh.* output directories, by editing the text files without renaming
> the directories.
>
> Hope this helps,
>
> a.y
>
> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers,
>>
>> I've got data pertaining to patients with left and right-sided temporal
>> lobe epilepsy (TLE).
>> My aim is to group those tracts according to side of epilepsy for
>> waypoint comparisons.
>>
>> Basically for patients with right TLE I'd like to look at right tracts
>> and at the same time for patients with left TLE I'd like to look at left
>> tracts (ipsilateral tracts), I need to do the same for the contralateral
>> tracts.
>> Is there a straightforward way of doing this?
>>
>> I've already copied the tracts to respective ipsi and contralateral
>> byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt;
>> do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in
>> R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i
>> ${i/byvoxel./byvoxel_contraRTLE.}; done
>> Now I have to flip the x-coordinates in the patients with right TLE (to
>> make them more comparable to the tracts of the patients with left TLE).
>> That will not be a problem, but I wonder if I am missing something?
>> Can I then just go ahead and run trac-all -stats -c dmrircfile to
>> generate the mean waypoint tracts etc.?
>>
>> Thank you very much,
>> Best wishes,
>>
>> Barbara
>>
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