Re: [Freesurfer] problem with mri_label2vol for aseg

[Bruce Fischl]

Hi Michelle

from the mri dir I think you can run:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz

-rl = "reslice like"
-rt = "resample type"

cheers
Bruce

p.s. I think your problem is probably that you used trilinear resampling. 
YOu could change the resampling in mri_vol2vol and it would work as well
On 
Sun, 15 Apr 2018, Michelle 
VanTieghem wrote:



Hi Freesurfer experts, 

I am trying to convert the aseg back into native space of the anatomical T1 
image. I followed the
instructions as in the webpage:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

specifically this line of code:

cd $SUBJECTS_DIR//mri
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz 
--regheader aseg.mgz
However, the result is very odd. The aseg boundaries appear correct in the 
subcortical regions.
however, at the gray mater boundaries, there are single voxels incorrectly 
labeled as different
subcortical-regions. As a result, in the viewer, the gray matter boundaries 
look multicolored. 

This is problematic, as I would like to extract a mask of specific ROIs (e.g. 
right amygdala) but
there are many other voxels labeled '54' in addition to the right amygdala. 

See attached images. I would greatly appreciate your assistance!! 

Thank you, 
Michelle 


--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu

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[Freesurfer] problem with mri_label2vol for aseg

[Michelle VanTieghem]

Hi Freesurfer experts,

I am trying to convert the aseg back into native space of the anatomical T1
image. I followed the instructions as in the webpage:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

specifically this line of code:

cd $SUBJECTS_DIR//mri
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
--regheader aseg.mgz

However, the result is very odd. The aseg boundaries appear correct in the
subcortical regions. however, at the gray mater boundaries, there are
single voxels incorrectly labeled as different subcortical-regions. As a
result, in the viewer, the gray matter boundaries look multicolored.

This is problematic, as I would like to extract a mask of specific ROIs
(e.g. right amygdala) but there are many other voxels labeled '54' in
addition to the right amygdala.

See attached images. I would greatly appreciate your assistance!!

Thank you,
Michelle


-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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[Freesurfer] reruns recon-all -long after edits

[Anna Daniels]

Dear FreeSurfer team,

using the longitudinal stream in v6.0.0, I edited the cross and base runs,
but still had to edit the long runs for some subjects. If I understood the
LongitudinalEdits Wiki correctly, the long can still be edited if
necessary.

Rerunning the respective recon-all command with -autorecon2 -autorecon3 and
the edited long run as input did not work. How do I rerun the
long correctly while incorporating the edits made directly to the long?

Here you see how I called the procedure:


anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
ls -lisa
total 20
8527874 4 drwxrwxr-x  5 anna anna 4096 Apr 15 21:18 .
8527873 4 drwxrwxr-x 34 anna anna 4096 Apr 15 12:18 ..
8544378 4 drwxrwxr-x 10 anna anna 4096 Mär 29 23:54 11904_base
8527875 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:02
11904_T1_fs_edit.long.11904_base_edit
8527888 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:29
11904_T2_fs_edit.long.11904_base_edit

anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
start=`date +%s`

anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
!recon
recon-all -long 11904_T1_fs_edit.long.11904_base 11904_base -autorecon2
-autorecon3

Unmatched ".

anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
end=`date +%s`

anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
runtime=$((end-start))

anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$
echo $runtime
10

As you can see, the process ends very quickly (10s) and only gives the
error 'Unmatched ".' though I did not open any double quotes when calling
the procedure.

Thanks a lot for your help!

Best,
Anna
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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

Hi Andrew, hi Bruce,

thanks for the tip! Unfortunately, the dev version of mri_normalize did not
work (resulted in the same error log) but simply manually checking the
control points in the respective cross runs and deleting the ones outside
the brain before rerunning worked!

Best,
Anna

2018-04-11 23:22 GMT+02:00 Bruce Fischl :

> p.s. you probably want to grab a new freeview also, as it lets you jump to
> the voxel coords of each control point so you can see them
>
> On Wed, 11 Apr 2018, Hoopes, Andrew wrote:
>
>
>> Hi Anna,
>>
>>
>>
>> You can download the new mri_normalize from this link -
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_
>> binaries/centos6_x86_64/mri_normalize
>>
>>
>>
>> To get it into your FS installation, first set executable permissions and
>> then move it into your
>> $FREESURFER_HOME/bin directory (sudo might be required):
>>
>>
>>
>> chmod +x /path/to/downloaded/mri_normalize
>>
>> mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/
>>
>>
>>
>> best
>>
>> Andrew
>>
>>
>>
>> From:  on behalf of Anna Daniels
>> 
>> Reply-To: FS Help 
>> Date: Monday, April 9, 2018 at 1:10 PM
>> To: FS Help 
>> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
>> peak at 110, cannot allocate
>> memory)
>>
>>
>>
>> Hi Bruce,
>>
>> thank you for the quick reply!
>>
>> Ubuntu 16.04 LTS 64-bit
>>
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>
>> Please let me know how to incorporate the new version into the
>> installation.
>>
>> Thank you very much and best,
>>
>> Anna
>>
>>
>>
>> Hi Anna
>>
>> no attachments :<
>>
>> Srishti's issue stemmed from control points outside of the head. The
>> current (dev) version of mri_normalize detects and removes them. Can you
>> grab a new version of mri_normalize and see if it fixes your problem? Let
>> us know your hardware/software environment and we will get it to you
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 6 Apr 2018, Anna Daniels wrote:
>>
>> > Hi Bruce, hi Srishti,
>> >
>> > I have exactly the same problem with several subjects rerunning
>> recon-all
>> > and there was sufficient memory available. I also tried out the last
>> command
>> > directly which resulted in the same error log.
>> >
>> > ?mri_normalize -f/home/anna/FREESURFER/00_DAT
>> A_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
>> > uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
>> > aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>> >
>> > Attached you can find the input file.
>> >
>> > Thank you and best,
>> > Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
>>
>>
>>
>>
>
> 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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