Re: [Freesurfer] reruns recon-all -long after edits

[Anna Daniels]

Hi Martin,

thank you so much for the quick and helpful reply!

As I only edited the wm.mgz in the base, there was still some non-wm
included there in the long and also some minor edits to the brainmask.mgz
were necessary that I had probably overlooked in the cross.

To run this command
recon-all -long 11904_T1_fs 11904_base  -autorecon2 -autorecon3

do I only need to have
11904_T1_fs.long.11904_base (the edited long) and
11904_base
in the subjects dir?

Or also the cross folder (11904_T1_fs)? I'm submitting the jobs from a HPC
system where the upload is time-consuming.

Thanks again!

Best,
Anna


---

Hi Anna,
yes, long can still be edited, but usually this is not necessary. What kind
of edits did you need to do in the long?

You would need to call with the long flag, and passing the cross and base
name. So just like the regular processing of the -long step, only replace
-all with -autorecon2 etc.

recon-all -long 11904_T1_fs 11904_base  -autorecon2 -autorecon3

for this to work 11904_T1_fs.long.11904_base
needs to contain your edits, so maybe backup the old long run and call it
backup, then edit this one and run it. You cannot simply append the _edit
or you will confuse the naming convention.

Best, Martin



> On 15. Apr 2018, at 23:07, Anna Daniels <anna.dani...@fu-berlin.de> wrote:
>
> 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 M?r 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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[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 <fis...@nmr.mgh.harvard.edu>:

> 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: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels
>> <anna.dani...@fu-berlin.de>
>> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, April 9, 2018 at 1:10 PM
>> To: FS Help <freesurfer@nmr.mgh.harvard.edu>
>> 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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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

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_DATA_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]
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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
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dispose of the e-mail.

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

[Anna Daniels]

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_DATA_MABT1T2/02a_MABT1T2_cross_
edits_transfer/rreruncrosstest_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​
 22275_T1_fs_edit.zip

​



> can you email us the input file and the full command line you ran?
> On Thu, 5
> Apr 2018, srishti goel wrote:
>
> > So it gave this error:
> >
> > 3d normalization pass 1 of 2
> >
> > white matter peak found at 110
> >
> > HISTOalloc(-2147483648): could not allocate histogram
> >
> > Cannot allocate memory
> >
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   let's see if it works. If it does, you should be able to run
> >
> >   recon-all -s SUBJID -make all
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > Should I re-run the recon-all after running the last command
> from recon-all.cmd?
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? Hi Srishti
> >
> > ? ? ? if you look in the subject's scripts dir there should
> be a file named "recon-all.cmd". Try
> > rerunning the last
> > ? ? ? command in it (probably from the mri dir)
> >
> > ? ? ? cheers
> > ? ? ? Bruce
> > ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? I am sorry, I am not sure what do you mean by
> running the command line directly?
> > ? ? ? ? ? ? I use the following command:
> >
> > ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END
> --mail-user srish...@email.unc.edu --wrap
> > "export
> > ? ? ? ? ? ? SUBJECTS_DIR=/proj/hng/sherida
> nlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166
> > ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa"
> >
> >
> > ? ? ? ? ? ? where sbatch. until export is our local
> server submission command and I run this
> > command from the
> > ? ? ? ? ? ? command line itself, not
> > ? ? ? ? ? ? using any script.
> >
> >
> > ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab
> > ? ? ? ? ? ? University of North Carolina at Chapel Hill
> > ? ? ? ? ? ? email (W): srish...@email.unc.edu
> > ? ? ? ? ? ? skype: srishti.goel12
> >
> >
> > ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? ? ? ? ? ? ? if you run the command that failed again
> on the command line directly (that is, not
> > in
> > ? ? ? ? ? ? recon-all) does it fail
> > ? ? ? ? ? ? ? ? ? again?
> >
> > ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce,
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run
> out of memory. Here is the memory usage
> > ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ?
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ?
> ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ?
> > ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available
> > ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ?
> 152102696 ? ? ? 12944 ? ?77294224 ?
> > ? ? ? ? ? ? ? ? ? ? ? ? 191963372
> > ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ?
> ? ? ? ? 2097148
> >
> >
> >
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life
> Experiences Lab
> > ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at
> Chapel