Re: [Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

[Yendiki, Anastasia]

Hi Katherine - If you mean the .trk format, that's not for storing labels, it's 
for storing tractography streamlines (i.e., a bunch of curves that are stored 
as sequences of x,y,z point coordinates). You can convert the FreeSurfer labels 
to nifti volumes, and see if the software that you're trying to use for graph 
analysis can read in the labels in that format.


TRACULA does not do whole brain tractography, it's for reconstructing specific 
pathways. If you want to do whole brain tensor tractography and save the 
results in .trk format, you can use the dtk/trackvis.


There are two different inputs that you need for your graph analysis, the 
tracts in .trk format and the labels that will be the end points of the tracts 
- you have to find out what the format of the latter needs to be.


a.y


From: Katherine Damme 
Sent: Thursday, February 22, 2018 8:45:20 PM
To: Anastasia Yendiki; Freesurfer support list
Subject: FreeSurfer Labels To Diffusion Toolkit/TrackVis

Hello Everyone,

I would like to use the FreeSurfer labels for fMRI and DTI in graph theory 
analyses. I am attempting to use UMPC to 
generate the graphs, which requires that the diffusion tensor imaging be in 
.dtk form. However, I have been struggling to get the FreeSurfer labels into 
the .dtk space.

While I have found this 
 
website suggesting a method for moving from the dtk space to FreeSurfer, it 
doesn't appear to be a reversible process.

Leading me to ask:

1. Is there a way to generate graphs from TRACULA?

or

2. How can I transform the labels or dlabels into dtk space?

Thank you for any help on this topic!

Kate Damme
___
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.

[Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

[Katherine Damme]

Hello Everyone,

I would like to use the FreeSurfer labels for fMRI and DTI in graph theory
analyses. I am attempting to use UMPC  to
generate the graphs, which requires that the diffusion tensor imaging be in
.dtk form. However, I have been struggling to get the FreeSurfer labels
into the .dtk space.

While I have found this
website
suggesting a method for moving from the dtk space to FreeSurfer, it doesn't
appear to be a reversible process.

Leading me to ask:

1. Is there a way to generate graphs from TRACULA?

or

2. How can I transform the labels or dlabels into dtk space?

Thank you for any help on this topic!

Kate Damme
___
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.

Re: [Freesurfer] Surface Errors

[Emily Schwartz]

Hi Doug, 

Attached are the point sets for the 3 subjects. For some issues, I put a range 
of coordinate points. Let me know if you need anything else.

Thanks! 

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, February 22, 2018 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

got em. can you send me coordinates (col, row,slice) where you are
seeing the errors? You can also create a point set in FreeView (under
File->New PointSet)


On 02/22/2018 08:48 AM, Emily Schwartz wrote:
> Hi Doug,
>
> Great, thank you. I sent it to you via filedrop.
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 4:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> yes, filedrop should be find
>
> thanks
>
>
> On 02/21/2018 04:44 PM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> I definitely can. I cannot use FTP from this computer for some reason. Can I 
>> upload it via filedrop and should I send it to your email?
>>
>> Thanks,
>>
>> Emily
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 4:29 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> I'm a little surprised you are getting them so frequently. Can you
>> upload a couple of subjects so I can take a look?
>>
>>
>>
>> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
>>> Hi Doug,
>>>
>>> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
>>> so often?
>>>
>>> Best,
>>>
>>> Emily
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 2:18 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> btw, what verions of FS are you using?
>>>
>>>
>>> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
 Got it, thank you so much!

 Best,

 Emily
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Wednesday, February 21, 2018 10:23 AM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Surface Errors

 Hi Emily

 it is a segmentation error, but it's a pretty small one. It will mess up
 the thickness in a region a few mm^2. You could fix it by editing the
 wm.mgz if you really care about that spot

 cheers
 Bruce


 On Wed, 21 Feb 2018, Emily Schwartz wrote:

> Hi Doug,
>
> Thank you for getting back to me. I've attached two images (Slice165 and 
> Slice166) with an arrow pointing to the location. I am new at this, so 
> maybe I am wrong and it is not a segmentation error.
>
> I've also attached an additional image (Slice185) of what I think is a 
> type of topological error that I often see multiple times in a subject. 
> Is this a topological defect? If so, if it is only over 3 slices does it 
> need to be corrected?
>
> Thanks again,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, February 20, 2018 4:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> sorry, what kind of errors? I could not really tell from the images what
> the problem was
>
>
> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>> Hi FreeSurfer community,
>>
>> I am working on elderly subjects and have had this kind of surface error 
>> quite often in different locations. Usually, it's over about 3-4 slices 
>> (in one view) and can be fixed, but I am finding multiple in almost 
>> every subject and therefore taking a lot of time to edit (and then once 
>> reprocessed new ones sometimes come up in different locations). I was 
>> wondering if these are normal to have, minor surface errors that do not 
>> necessarily need to be fixed. I have added images of an example below. 
>> Here are some of the values I get from aparc.stats for caudal middle 
>> frontal lh after manually editing:
>>
>> Surface area:
>> Original - 2500 mm^2

Re: [Freesurfer] Update: asymmetric parcellation error

[Douglas N Greve]

don't know. can you send these subjects to me through our filedrop? url 
below


On 02/22/2018 11:39 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
> Dear Freesurfer developers,
>
> When I was troubleshooting my data I came across an odd parcellation 
> error that I can not place. When looking at the reconstructed surface 
> parcellation (freeview -f 
>  {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ 
> --viewport 3d)  I noticed that in a large proportion of my subjects 
> the parcellated errors are not placed correctly. Moreover, the error 
> mostly seems to apply to the right cortex and not the left. I adjusted 
> foto's for visual information.
>
> I already checked the brain mask.mgz file and the rh.white and rh.pial 
> surfaces I cannot find any segmentation errors either.
>
> Do you have any idea what could have gone wrong and how I can correct 
> for this?
>
> Kind regards,
> Aicha
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] Surface Errors

[Douglas N Greve]

got em. can you send me coordinates (col, row,slice) where you are 
seeing the errors? You can also create a point set in FreeView (under 
File->New PointSet)


On 02/22/2018 08:48 AM, Emily Schwartz wrote:
> Hi Doug,
>
> Great, thank you. I sent it to you via filedrop.
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 4:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> yes, filedrop should be find
>
> thanks
>
>
> On 02/21/2018 04:44 PM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> I definitely can. I cannot use FTP from this computer for some reason. Can I 
>> upload it via filedrop and should I send it to your email?
>>
>> Thanks,
>>
>> Emily
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 4:29 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> I'm a little surprised you are getting them so frequently. Can you
>> upload a couple of subjects so I can take a look?
>>
>>
>>
>> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
>>> Hi Doug,
>>>
>>> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
>>> so often?
>>>
>>> Best,
>>>
>>> Emily
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 2:18 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> btw, what verions of FS are you using?
>>>
>>>
>>> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
 Got it, thank you so much!

 Best,

 Emily
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Wednesday, February 21, 2018 10:23 AM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Surface Errors

 Hi Emily

 it is a segmentation error, but it's a pretty small one. It will mess up
 the thickness in a region a few mm^2. You could fix it by editing the
 wm.mgz if you really care about that spot

 cheers
 Bruce


 On Wed, 21 Feb 2018, Emily Schwartz wrote:

> Hi Doug,
>
> Thank you for getting back to me. I've attached two images (Slice165 and 
> Slice166) with an arrow pointing to the location. I am new at this, so 
> maybe I am wrong and it is not a segmentation error.
>
> I've also attached an additional image (Slice185) of what I think is a 
> type of topological error that I often see multiple times in a subject. 
> Is this a topological defect? If so, if it is only over 3 slices does it 
> need to be corrected?
>
> Thanks again,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, February 20, 2018 4:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> sorry, what kind of errors? I could not really tell from the images what
> the problem was
>
>
> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>> Hi FreeSurfer community,
>>
>> I am working on elderly subjects and have had this kind of surface error 
>> quite often in different locations. Usually, it's over about 3-4 slices 
>> (in one view) and can be fixed, but I am finding multiple in almost 
>> every subject and therefore taking a lot of time to edit (and then once 
>> reprocessed new ones sometimes come up in different locations). I was 
>> wondering if these are normal to have, minor surface errors that do not 
>> necessarily need to be fixed. I have added images of an example below. 
>> Here are some of the values I get from aparc.stats for caudal middle 
>> frontal lh after manually editing:
>>
>> Surface area:
>> Original - 2500 mm^2
>> Edited -  2532 mm^2
>>
>> Grey volume:
>> Original -  1710 mm^3
>> Edited -  1727 mm^3
>>
>> Thickness avg
>> Original -  4455 mm  std: 2.371
>> Edited -  4445 mm  std: 2.365
>>
>> Although the thickness values only differ by 10 mm, we are a little 
>> concerned because the difference is not within the standard deviation.
>>
>> Please let me know if all of these errors should be edited or if it may 
>> be 

Re: [Freesurfer] Freesurfer equivalent to fslmaths?

[Bruce Fischl]

Hi Jared

what are the exact command lines you ran? I don't think it can be a 
freeview problem if the overlays are different.


cheers
Bruce
On Wed, 21 Feb 2018, 
Zimmerman, Jared wrote:




Hey Doug, Bruce, et al., any update on why fscalc and Matlab are not producing 
the same values when
trying to run a mean?  I’m using fscalc to pilot some stuff now, but not sure 
if I should be
trusting the values I’m getting out of it.

 

It seems this issue might be caused by how Freeview is reading the images and 
not by either Matlab
or fscalc.  See the screenshot below.  The two overlays loaded in Freeview 
should be the exact same
image, which is the mean of three other images, one calculated with fscalc 
(*smMean246.mgh) and the
other by reading the images into Matlab (*matlab_lh.mgh).  Notice that at the 
crosshair (vertex
37431) the values in the two overlays are different by ~0.03, or ~3.5%. 

 

However, if I read these two images into Matlab with MRIread() and look at that 
vertex, both images
have the same value, which is 1.9042

 

So it seems like maybe Freeview and Matlab are not reporting the same values 
for the images, and
possibly the images I write in Matlab are somehow getting depressed by 
Freeview.  I’m not able to
stay connected to my cluster for much longer than 10-15 min at the moment, so 
it’s hard for me to
troubleshoot more, but I can provide sample images and code to recreate the 
problem tomorrow.

 

Is this a known issue that somehow images written in Matlab are not read 
properly by Freeview?

 

This is on v5.3.0 and Matlab 2014b.  I can try tomorrow if the issue persists 
in v6.0

 

Thanks,

Jared

 

 

 

[IMAGE]

 

 

From:  on behalf of "Zimmerman, Jared"

Reply-To: Freesurfer support list 
Date: Friday, February 16, 2018 at 2:12 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer equivalent to fslmaths?

 

Thanks Doug and Bruce, 

 

Fscalc is great because I can do maths with multiple inputs, like a mean.  I’m 
noticing, however,
that when I do a mean with fscalc I get different values than when I do the 
mean in Matlab, any idea
why?  In some regions the differences are as much as 5-10% so I don’t think 
it’s just a
rounding/precision issue.

 

fscalc a.mgh add b.mgh add c.mgh add d.mgh add e.mgh div 5 --odt float --o 
mean.mgh

 

Hard to imagine it’s an order of operations issue, but I am a little confused 
about how fscalc
handles order of operations from the help page.

 

I’m using v5.3.0 and Matlab 2014b

 

Thanks,

Jared

 

From:  on behalf of Douglas Greve

Reply-To: Freesurfer support list 
Date: Friday, February 16, 2018 at 11:31 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Freesurfer equivalent to fslmaths?

 

Or fscalc

 

On 2/16/18 11:22 AM, Bruce Fischl wrote:

  Hi Jared

  I think mris_calc does at least some of what you want.

  cheers
  Bruce
  On Fri, 16 Feb 2018, Zimmerman, Jared wrote:




Hi all,

 

Is there an equivalent of fslmaths in Freesurfer?  I would like to 
add two
scalar value images (.mgh
files) that are registered to the fsaverage6 surface but I’m not 
seeing an
obvious way to do it. 
Right now I’m reading the images into Matlab to add them, but this 
is a bit
inconvenient because
what I would like to do is smooth an image by a small amount, add 
the
original image back to it,
then smooth again marginally and iterate until I get to a target 
fwhm. 
Since I can’t smooth inside
Matlab this necessitates writing out a temp image for each 
smoothing step
then reading it back into
Matlab for the adding.  Obviously this is a solvable problem, but 
as someone
only marginally
proficient in Matlab it’s something I’d like to avoid, plus it 
seems like a
lot of I/O for this
task.

 

A little more detail on my data and what I’m trying to do:

 

The scalar images I’m working with are network confidence maps, 
basically
like the spatial maps from
an ICA dual-regression.  I want to combine the confidence maps 
together into
a hard partition and
write it to an annot file, but I want to smooth them first.  I’m 
concerned,
however, that smoothing
is going to bias the parcellation against small network parcels and 
in favor
of large network
parcels because in each confidence map the small parcels will be 
surrounded
by lots of zeros (does

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

[Martin Reuter]

Could be all that is needed is to add this:


mycluster ='sbatch --mail-type=FAIL --mail-user= -N 1 
--ntasks-per-node=10 --partition=work --export=ALL -o 
/%(username)s/logs/job.%J.out- e 
/%(username)/logs/job.%J.err "%(command)s"'


and comment the lines

# if queue is not None ...
#   pbcmd = ...

with a hashtag.

you can also simplify the slurm command (remove the --mail flags and the 
-o logfile location flags) your cluster partition may not be called 
"work" either.


Best, Martin


Am 22.02.2018 um 16:43 schrieb Martin Reuter:


Hi Lea,


I wrote that script to simplify processing on our cluster which uses 
qsub PBS for submission. I have never used SLURM so far.



There is two functions that you (or someone who knows this stuff) 
would need to modify:


def submit

and

def wait_jobs


The submit procedure basically issues a submit command (stored in 
pbcmd).  The examples there should help anyone who programs python to 
modify it for a slurm submission.



The wait_jobs scripts runs a different command (here qstat and grep 
user) to see how many jobs you are already running and waits until 
this number sinks below maxjobs, then it continues submitting new 
jobs. If you don't care about the number of submitted jobs (because 
your cluster does the scheduling anyway), you can just write



"return" as the first line (before the "users = os." line).


Still the submit block would have to be rewritten for slurm.


Best, Martin



Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:

Dear FS experts,

I am trying to do a longitudinal analysis of around 250 adolescents 
with up to 4 data points each. Given the complexity I would like to 
use the long_submit_jobs script which is described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts 



Unfourtunately it does only run on launchpad and I would do the 
analyses with SLURM using bash system.
Has anybody adopted the script so i will run with SLURM or does 
anybody know where I should look to get information on this?


I have little scripting experience so any help would be greatly 
appreciated!


Best,

Lea Backhausen, B.Sc.

Research assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und 
–psychotherapie

Tel. +49 (0)351 458-7166
Fax +49 (0)351 458-5754

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
*MailScanner has detected a possible fraud attempt from 
"deref-web-02.de" claiming to be* _http://www.uniklinikum-dresden.de_ 


Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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.

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

[Satrajit Ghosh]

hi lea,

in addition you could consider using the bids app for freesurfer:
https://github.com/BIDS-Apps/freesurfer

and then submit each subject's longitudinal pipeline as a separate slurm
job.

cheers,

satra

On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter  wrote:

> Hi Lea,
>
>
> I wrote that script to simplify processing on our cluster which uses qsub
> PBS for submission. I have never used SLURM so far.
>
>
> There is two functions that you (or someone who knows this stuff) would
> need to modify:
>
> def submit
>
> and
>
> def wait_jobs
>
>
> The submit procedure basically issues a submit command (stored in pbcmd).
> The examples there should help anyone who programs python to modify it for
> a slurm submission.
>
>
> The wait_jobs scripts runs a different command (here qstat and grep user)
> to see how many jobs you are already running and waits until this number
> sinks below maxjobs, then it continues submitting new jobs. If you don't
> care about the number of submitted jobs (because your cluster does the
> scheduling anyway), you can just write
>
>
> "return" as the first line (before the "users = os." line).
>
>
> Still the submit block would have to be rewritten for slurm.
>
>
> Best, Martin
>
>
>
> Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:
>
> Dear FS experts,
>
> I am trying to do a longitudinal analysis of around 250 adolescents with
> up to 4 data points each. Given the complexity I would like to use the
> long_submit_jobs script which is described here: https://surfer.nmr.mgh.
> harvard.edu/fswiki/FsTutorial/Scripts
>
> Unfourtunately it does only run on launchpad and I would do the analyses
> with SLURM using bash system.
> Has anybody adopted the script so i will run with SLURM or does anybody
> know where I should look to get information on this?
>
> I have little scripting experience so any help would be greatly
> appreciated!
>
> Best,
>
> Lea Backhausen, B.Sc.
>
> Research assistant
>
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie
> Tel. +49 (0)351 458-7166 <+49%20351%204587166>
> Fax +49 (0)351 458-5754 <+49%20351%204585754>
>
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> *MailScanner has detected a possible fraud attempt from "deref-web-02.de"
> claiming to be* *http://www.uniklinikum-dresden.de*
> 
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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.
>
>
___
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.

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

[Martin Reuter]

Hi Lea,


I wrote that script to simplify processing on our cluster which uses 
qsub PBS for submission. I have never used SLURM so far.



There is two functions that you (or someone who knows this stuff) would 
need to modify:


def submit

and

def wait_jobs


The submit procedure basically issues a submit command (stored in 
pbcmd).  The examples there should help anyone who programs python to 
modify it for a slurm submission.



The wait_jobs scripts runs a different command (here qstat and grep 
user) to see how many jobs you are already running and waits until this 
number sinks below maxjobs, then it continues submitting new jobs. If 
you don't care about the number of submitted jobs (because your cluster 
does the scheduling anyway), you can just write



"return" as the first line (before the "users = os." line).


Still the submit block would have to be rewritten for slurm.


Best, Martin



Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:

Dear FS experts,

I am trying to do a longitudinal analysis of around 250 adolescents 
with up to 4 data points each. Given the complexity I would like to 
use the long_submit_jobs script which is described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts 



Unfourtunately it does only run on launchpad and I would do the 
analyses with SLURM using bash system.
Has anybody adopted the script so i will run with SLURM or does 
anybody know where I should look to get information on this?


I have little scripting experience so any help would be greatly 
appreciated!


Best,

Lea Backhausen, B.Sc.

Research assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und 
–psychotherapie

Tel. +49 (0)351 458-7166
Fax +49 (0)351 458-5754

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
*MailScanner has detected a possible fraud attempt from 
"deref-web-02.de" claiming to be* _http://www.uniklinikum-dresden.de_ 


Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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.

Re: [Freesurfer] Problem with cortical parcellation of rh but not lh

[Amal Achaibou]

Hi Bruce,

I sent you two subject's directories through FileDrop.

Thanks!


Cheers


Amal



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, February 21, 2018 6:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh

Hi Amal

we need the entire directory tree for that subject
cheers
Bruce
On Wed, 21 Feb 2018, Amal
Achaibou wrote:

>
> Hi,
>
> Yes I've seen it for multiple subjects.
>
> I'm using version 6.
>
> Here are the results for one participants, let me know if you need any other 
> file.
>
> Thanks
>
>
> Amal
>
>
>
>
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Bruce Fischl 
> Sent: Thursday, February 15, 2018 8:37 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh
> Hi Amal
>
> this happens for multiple subjects? What version are you using? I have
> only ever seen this very rarely and usually for an atypical (e.g.
> multiple central sulci) folding pattern. Can you upload a subject so I
> can take a look?
>
> cheers
> Bruce
> On Tue, 13 Feb 2018, Amal Achaibou wrote:
>
> >
> > Hello,
> >
> > I'm new to freesurfer and have been trying to use it for cortical 
> > parcellation of individual T1s
> > running recon-all -s subID -i sunT1 -all command. I'm specifically 
> > interested in getting
> > parahippocampal and perirhinal ROIs for each individual. It appears that 
> > the parcellation is
> correct
> > for the left hemisphere but not for the right hemisphere... I found that 
> > there were also
> mislabeling
> > for precentral and postcentral gyrus (as easy gyri to identify), and that 
> > regardless of if I
> looked
> > at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme.
> >
> > Is there any reason why I have this systematic mistake? Attached is the 
> > example for one subject
> > (others looked very similar).
> >
> >
> > Thanks
> >
> >
> > Amal
> >
> >
> >___
> _
> >
> >
> >
> ___
> 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.
>
>
>
___
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.

Re: [Freesurfer] Surface Errors

[Emily Schwartz]

Hi Doug, 

Great, thank you. I sent it to you via filedrop.

Best,

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 21, 2018 4:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

yes, filedrop should be find

thanks


On 02/21/2018 04:44 PM, Emily Schwartz wrote:
> Hi Doug,
>
> I definitely can. I cannot use FTP from this computer for some reason. Can I 
> upload it via filedrop and should I send it to your email?
>
> Thanks,
>
> Emily
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 4:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> I'm a little surprised you are getting them so frequently. Can you
> upload a couple of subjects so I can take a look?
>
>
>
> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
>> so often?
>>
>> Best,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 2:18 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> btw, what verions of FS are you using?
>>
>>
>> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
>>> Got it, thank you so much!
>>>
>>> Best,
>>>
>>> Emily
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 10:23 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> Hi Emily
>>>
>>> it is a segmentation error, but it's a pretty small one. It will mess up
>>> the thickness in a region a few mm^2. You could fix it by editing the
>>> wm.mgz if you really care about that spot
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>>>
 Hi Doug,

 Thank you for getting back to me. I've attached two images (Slice165 and 
 Slice166) with an arrow pointing to the location. I am new at this, so 
 maybe I am wrong and it is not a segmentation error.

 I've also attached an additional image (Slice185) of what I think is a 
 type of topological error that I often see multiple times in a subject. Is 
 this a topological defect? If so, if it is only over 3 slices does it need 
 to be corrected?

 Thanks again,

 Emily
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, February 20, 2018 4:59 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Surface Errors

 sorry, what kind of errors? I could not really tell from the images what
 the problem was


 On 02/20/2018 10:22 AM, Emily Schwartz wrote:
> Hi FreeSurfer community,
>
> I am working on elderly subjects and have had this kind of surface error 
> quite often in different locations. Usually, it's over about 3-4 slices 
> (in one view) and can be fixed, but I am finding multiple in almost every 
> subject and therefore taking a lot of time to edit (and then once 
> reprocessed new ones sometimes come up in different locations). I was 
> wondering if these are normal to have, minor surface errors that do not 
> necessarily need to be fixed. I have added images of an example below. 
> Here are some of the values I get from aparc.stats for caudal middle 
> frontal lh after manually editing:
>
> Surface area:
> Original - 2500 mm^2
> Edited -  2532 mm^2
>
> Grey volume:
> Original -  1710 mm^3
> Edited -  1727 mm^3
>
> Thickness avg
> Original -  4455 mm  std: 2.371
> Edited -  4445 mm  std: 2.365
>
> Although the thickness values only differ by 10 mm, we are a little 
> concerned because the difference is not within the standard deviation.
>
> Please let me know if all of these errors should be edited or if it may 
> be okay to keep the smaller segmentation/topological errors as they are.
>
> Thank you,
>
> Emily
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 

[Freesurfer] Unknown Label in following postprocessing with mne-python

[Daniel van de Velden]

Dear fellow colleagues,


in my study I use volumetric source spaces. In the process of creating 
them, I decided to identify all available volumelabels FreeSurfer 
"recognized" in the given mri image.

Every single subject inherits, despite all other volumelabels, a 
volumelabel called "Unknown". In an 3D representation of those "unknown" 
volumelabel coordinates I opine those points could also be part of other 
volumelabels like cerebral cortex or white matter.

Would you please give me a detailed explanation of the origin of this 
'Unknown' label? Specifically in respect to the fsaverage "subject".


Best regards,

Daniel van de Velden

___
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.