Re: [Freesurfer] Error in Reconstruction of bert samples.

[Allison Moreau]

Hi,


It looks like Freesurfer can't read bert's brainmask.mgz volume. Can you 
ls -l bert's mri directory and see if that file is there and you have 
proper permission to read it? mri_watershed is looking for that file 
because the command says to keep the edits from brainmask.mgz, but that 
file is normally generated after the watershed step that is failing and 
I don't see any previous instances of recon-all in the log file where 
brainmask.mgz was created.



Best,

Allison


On 03/20/2017 02:05 AM, IPL Neurosurgery wrote:
IPL Neurosurgery has shared a OneDrive file with you. To view it, 
click the link below.




recon-all 1.log 
[recon-all 1.log]

Hi,


We have encountered a error in skull stripping process in bert sample. 
We are a novice. We attached the log.



*Command :* recon-all -s bert -all


#@# Skull Stripping Sat Mar 18 14:58:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri

 mri_watershed -rusage 
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat 
-keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas 
/home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz



Keeping brain edits brainmask.auto.mgz brainmask.mgz
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for 
details)
mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, 
-1): read error


*
The input file is T1.mgz
The output file is brainmask.auto.mgz
No such file or directory
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 
18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017

*freesurfer version:* 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c



*Platform: *Cent OS 7


*uname -a* *: *3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Any Suggestion will be appreciated.


Thanking you,


IPL Neurosurgery.



Sent from Outlook 



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Re: [Freesurfer] Recon-all

[Allison Moreau]

Hi Heidi,

Once 6.0 is released and you have installed it, you can simply source 
that version of FreeSurfer and rerun your subjects the same way you did 
for 5.3.


Best,
Allison

On 08/12/2016 06:02 AM, Heidi Foo wrote:

Hi FreeSurfer Team,

I have done recon-all using FS 5.3 and I would like to run the 
recon-ed images from 5.3 in FS 6.0. May I know how I should go about 
doing that?


Thank you.

Regards,
Heidi Foo


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[Freesurfer] September FreeSurfer Course in Boston Registration open

[Allison Moreau]

The FreeSurfer group is offering a four-day FreeSurfer Tutorial and 
Workshop September 26th to 29th, 2016 at the Martinos Center in 
Charlestown, MA. You can register for the course on our course website: 
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription

Details about the content of the course, the location, registration 
fees, accepted payment types, and nearby hotels is currently on the 
website above. Please read the above page in its entirety before 
registering and before sending questions.

If you are not one of the first 50 to register, you will be put on a 
waiting list and will be notified if a spot becomes available. *Do not 
submit a payment or make travel arrangements until you have received an 
email confirmation that you successfully secured a seat in the course.

*NOTE- We will hold the course even if 40 students are not registered, 
so you can make travel arrangements once you have received an email 
confirmation.
-- 
Allison Moreau
Research Technologist
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

[Allison Moreau]

Hi Falk and Thomas,

We are actually working on testing the -hires flag now for the v6 
release. We intend to release it with v6.


-Allison

On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:


Hi Thomas,

this looks like a really nice script and a lot better than my own. In 
the upcoming release of FreeSurfer v.6 my work-around probably is not 
needed anymore. However, I haven’t been able to have a look at the dev 
release yet and whether the standard recon-all features a flag to 
process high resolution data.


Best,

Falk

P.S. Following your instructions one will definitely become a coffee 
junkie. :D


*Von:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag **von 
*Emmerling Thomas (PSYCHOLOGY)

*Gesendet:* Mittwoch, 24. Juni 2015 14:35
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

Hello!

I wrote a bash script some time ago to process data acquired at a 
sub-millimeter resolution following the nice wiki entry of Falk 
Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I 
thought it might be helpful for others, too, as there are some 
questions about it in the mailing list archives, so here it is: 
https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy 
about any comments!


Best,

Thomas



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Re: [Freesurfer] WM Edits not updating in batch

[Allison Moreau]

Hi Matt,

Could you upload that subject to our filedrop and I will take a look. 
https://gate.nmr.mgh.harvard.edu/filedrop2/


-Allison

On 06/12/2015 01:04 AM, Matthew Peverill wrote:

(I'm working with Kate on this one)

The problem is with the white matter surface. The pial surface is 
usually fine, but the white matter boundary doesn't budge. I've 
attached the image. Thanks for your help!

-Matt

On Thu, Jun 11, 2015 at 12:42 PM, Allison Moreau 
almor...@nmr.mgh.harvard.edu mailto:almor...@nmr.mgh.harvard.edu 
wrote:


Hi Kate,

I am having trouble viewing the image. Could you send it as an
attachment?

When you say main surface, are you referring to the pial or white
surface?

-Allison


On 06/11/2015 03:07 PM, McLaughlin, Katie wrote:

Hello Freesurfer Experts,

I'm trying to troubleshoot a problem where the main surface in
our brains is not adjusting following white matter edits using
Freesurfer 5.3. To be clear, the procedure here is:

1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3

Following this process, what we see is that the main surface in
the brain still encompasses areas that were deleted from wm.mgz.
Here is an example (at bottom of the inferior temporal lobe):
Inline image 1


This seems to be true for all the edits we've made on this set of
brains.

There are no errors in recon-all.log, and the right brain is
being recon'd. Files in the surf directory seem to be updated as
expected. Any idea what we're missing here? We haven't had
trouble with this process in the past. Any help would be much
appreciated!

Thanks,
Kate



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--
Matthew Peverill
857-277-9083
mrpever...@gmail.com mailto:mrpever...@gmail.com (preferred)


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Re: [Freesurfer] WM Edits not updating in batch

[Allison Moreau]

Hi Kate,

I am having trouble viewing the image. Could you send it as an attachment?

When you say main surface, are you referring to the pial or white surface?

-Allison

On 06/11/2015 03:07 PM, McLaughlin, Katie wrote:

Hello Freesurfer Experts,

I'm trying to troubleshoot a problem where the main surface in our 
brains is not adjusting following white matter edits using Freesurfer 
5.3. To be clear, the procedure here is:


1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3

Following this process, what we see is that the main surface in the 
brain still encompasses areas that were deleted from wm.mgz. Here is 
an example (at bottom of the inferior temporal lobe):

Inline image 1


This seems to be true for all the edits we've made on this set of brains.

There are no errors in recon-all.log, and the right brain is being 
recon'd. Files in the surf directory seem to be updated as expected. 
Any idea what we're missing here? We haven't had trouble with this 
process in the past. Any help would be much appreciated!


Thanks,
Kate



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