[Freesurfer] combine orthogonal stacks
External Email - Use Caution Dear Experts, I don't know if this is even possible, but I'm hoping you can help. I have 3 clinical T1 scans in NIFTI format: one has good resolution in the axial plane one has good resolution in the coronal plane one has good resolution in the sagittal plane My dream is to combine the 3 orthogonal planes into a single high-resolution 3d image. Is such a thing possible? Does anyone have suggestions? Thanks so much, Dianne -- Dianne Patterson, Ph.D. Research Scientist d...@email.arizona.edu or dianne...@gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) == If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. == Antipiphany: That moment when you realize how little you actually know == ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer License issue
External Email - Use Caution Hi, Here's what I've learned from my attempts (eventually successful), to run freesurfer in docker on a mac: There are three tricks to running the freesurfer *docker* container. 1) You must request a license.txt file from the freesurfer website: https://surfer.nmr.mgh.harvard.edu/fswiki/License 2) You must bind mount the license file on the outside to license.txt on the inside of the container (this is just like binding the input small_ds and outputs directories), e.g.: >docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v /Volumes/Main/Working/BIDS_TESTING/small_ds:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file /license.txt 3) On the mac, Docker runs in a minimal virtual machine. By default, this machine is allowed to access 2 GB of RAM. recon-all requires more RAM (~4 GB or more) https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements. See instructions here for increasing the RAM on Docker for Mac: https://docs.docker.com/docker-for-mac/#advanced On Fri, Jul 20, 2018 at 1:13 AM Carolina Bonivento < boniventocarol...@gmail.com> wrote: > External Email - Use Caution > > Apologize, I forgot to attach the file with the license. Here it is. > > Best regards, > > Carolina > > > > > Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento < > boniventocarol...@gmail.com> ha scritto: > > Dear Sir/Madame, > I recently subscribed the FS license (attached) but when I tried to run > the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I > received the following error message: > > *ERROR: Invalid FreeSurfer license key found in license file > /root/freesurfer/license.txt* > > Following some instruction that I got previously, I replaced the .license > with the license.txt in the $FREESURFER_HOME directory (in my case > root/freesurfer) but I still get the same error message. > > Note that I’m running FreeSurfer through a Docker container running > Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a > macOS High Sierra (of course, Docker and the freesurfer folder are on the > same machine). When I filled the license request form I’ve selected > Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker > container. Is it possible that the issue is due to this? In that case, can > I ask for a second license? > > Thank you in advance for your attention. > > Looking forward to hearing from you, I’m sending you my best regards, > > Carolina > > > ___ > 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. > -- Dianne Patterson, Ph.D. Research Scientist d...@email.arizona.edu or dianne...@gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) == If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. == Antipiphany: That moment when you realize how little you actually know == ___ 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] [bids-discussion] freesurfer bids container fails to find license file
Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that makes it happy. -Dianne On Sun, Feb 4, 2018 at 10:52 AM, Chris Gorgolewski < krzysztof.gorgolew...@gmail.com> wrote: > This looks like a memory issue to me as indicated bu those two lines: > > /opt/freesurfer/bin/reconbatchjobs: line 81: 4014 Killed > exec $JOB >> $LOG 2>&1 > /opt/freesurfer/bin/reconbatchjobs: line 81: 4017 Killed > exec $JOB >> $LOG 2>&1 > > You can adjust how much memory of your host machine will be accessible to > your docker containers. More details here: https://docs.docker.com/ > docker-for-mac/#memory > > Best, > Chris > > On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson <d...@email.arizona.edu> > wrote: > >> Dear All, >> Pardon my ignorance. I am trying freesurfer for the first time, using >> the BIDS docker container and the standard dataset ds005. >> Although I have specified 2 participants to run, freesurfer exits with >> errors after the first (and does the same if I run the 2nd subject >> separately). >> I am attaching the 3 logs which I take to be most relevant. I'd be happy >> to provide other logs if they would be useful for understanding the >> problem. >> Any insight into why this is happening would be much appreciated. >> >> Thanks, >> >> Dianne >> >> On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski < >> krzysztof.gorgolew...@gmail.com> wrote: >> >>> This is not expected. >>> >>> You would need to provide more details (recon-all.log) for anyone to be >>> able to help you. It might be also worth googling the specific error >>> message before hand - it could be that someone else run into this before. >>> >>> Best, >>> Chris >>> >>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson <d...@email.arizona.edu> >>> wrote: >>> >>>> Since I'm following the example on the github page, using the ds005 >>>> dataset, now with the correct license binding, I am surprised to see >>>> freesurfer exiting with errors (but I don't know much about freesurfer): >>>> >>>> I run this: >>>> >>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_TES >>>> TING/license.txt:/license.txt:ro -v >>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro >>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer >>>> /bids_dataset /outputs participant --participant_label 01 02 --license_file >>>> /license.txt >>>> >>>> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb 4 >>>> 03:27:11 UTC 2018 >>>> And then sub-02 does not run >>>> >>>> Is this what I should expect? >>>> >>>> Thanks, >>>> >>>> Dianne >>>> >>>> >> >> >> -- >> Dianne Patterson, Ph.D. >> Research Scientist >> d...@email.arizona.edu <d...@u.arizona.edu> >> or >> dianne...@gmail.com >> University of Arizona >> Speech and Hearing Science 314 >> 1131 E 2nd Street, Building #71 >> <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371=gmail=g> >> (Just East of Harvill) >> == >> If you don't hear back from me (and you expected to), >> I blame the University's new SPAM filter. >> Please write to my gmail account. >> == >> Antipiphany: That moment when you realize how little you actually know >> == >> >> -- >> You received this message because you are subscribed to the Google Groups >> "bids-discussion" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to bids-discussion+unsubscr...@googlegroups.com. >> To post to this group, send email to bids-discuss...@googlegroups.com. >> To view this discussion on the web visit https://groups.google.com/d/ms >> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L >> 0iEgFiUQQdqvw%40mail.gmail.com >> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L0iEgFiUQQdqvw%40mail.gmail.com?utm_medium=email_source=footer> >> . >> >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "bids-discussion" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to bids-discussion+unsu
Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file
Since I'm following the example on the github page, using the ds005
dataset, now with the correct license binding, I am surprised to see
freesurfer exiting with errors (but I don't know much about freesurfer):
I run this:
docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v
/Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
/Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset /outputs participant --participant_label 01 02 --license_file
/license.txt
A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb 4
03:27:11 UTC 2018
And then sub-02 does not run
Is this what I should expect?
Thanks,
Dianne
On Mon, Jan 22, 2018 at 9:54 PM, Dianne Patterson <d...@email.arizona.edu>
wrote:
> Wonderful...and makes total sense! Thankyou...it is off and running now.
> -Dianne
>
>
> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
> krzysztof.gorgolew...@gmail.com> wrote:
>
>> Hi Dianne,
>>
>> You need to "mount" the using -v the same way input and output
>> directories are mounted. For example:
>>
>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
>> TESTING/license.txt:/license.txt:ro -v
>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>> /bids_dataset /outputs participant --license_file /license.txt
>>
>> Best,
>> Chris
>>
>> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson <d...@email.arizona.edu>
>> wrote:
>>
>>> Dear All,
>>>
>>> After trying the example bids app (which worked fine), I am trying the
>>> freesurfer bids app. I have built the docker container on my mac and I have
>>> the ds005 data directory here and the license.txt which I requested from
>>> freesurfer.
>>> I asked for a linux license (assuming the container contains linux and
>>> that was the relevant fact).
>>>
>>> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
>>> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file "license.txt"
>>> 1: You should define 'SliceTiming' for this file. If you don't provide
>>> this information slice time correction will not be possible. (code: 13 -
>>> SLICE_TIMING_NOT_DEFINED)
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
>>> ... and 38 more files having this issue (Use --verbose to see them all).
>>>
>>> Summary: Available Tasks: Available
>>> Modalities:
>>> 133 Files, 1.77GBmixed-gambles taskT1w
>>> 16 - Subjects inplaneT2
>>> 1 - Sessionbold
>>>
>>>
>>> Traceback (most recent call last):
>>> File "/run.py", line 165, in
>>> raise Exception("Provided license file does not exist")
>>> *Exception: Provided license file does not exist*
>>> ===
>>> If I provide the full path to the license file, it still fails:
>>>
>>> docker run -ti --rm -v
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file
>>> "/Volumes/Main/Working/BIDS_TESTING/license.txt"
>>>
>>> Suggestions? How do I tell freesurfer where the license file is?
>>>
>>> Thanks so much,
>>>
>>> Dianne
>>>
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> Research Scientist
>>> d...@email.arizona.edu <d...@u.arizona.edu>
>>> or
>>> dianne...@gmail.com
>>> University of
Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file
Wonderful...and makes total sense! Thankyou...it is off and running now.
-Dianne
On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
krzysztof.gorgolew...@gmail.com> wrote:
> Hi Dianne,
>
> You need to "mount" the using -v the same way input and output directories
> are mounted. For example:
>
> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
> TESTING/license.txt:/license.txt:ro -v
> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
> /bids_dataset /outputs participant --license_file /license.txt
>
> Best,
> Chris
>
> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson <d...@email.arizona.edu>
> wrote:
>
>> Dear All,
>>
>> After trying the example bids app (which worked fine), I am trying the
>> freesurfer bids app. I have built the docker container on my mac and I have
>> the ds005 data directory here and the license.txt which I requested from
>> freesurfer.
>> I asked for a linux license (assuming the container contains linux and
>> that was the relevant fact).
>>
>> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
>> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>> /bids_dataset /outputs participant --license_file "license.txt"
>> 1: You should define 'SliceTiming' for this file. If you don't provide
>> this information slice time correction will not be possible. (code: 13 -
>> SLICE_TIMING_NOT_DEFINED)
>> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
>> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
>> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
>> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
>> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
>> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
>> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
>> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
>> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
>> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
>> ... and 38 more files having this issue (Use --verbose to see them all).
>>
>> Summary: Available Tasks: Available
>> Modalities:
>> 133 Files, 1.77GBmixed-gambles taskT1w
>> 16 - Subjects inplaneT2
>> 1 - Sessionbold
>>
>>
>> Traceback (most recent call last):
>> File "/run.py", line 165, in
>> raise Exception("Provided license file does not exist")
>> *Exception: Provided license file does not exist*
>> ===
>> If I provide the full path to the license file, it still fails:
>>
>> docker run -ti --rm -v
>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>> /bids_dataset /outputs participant --license_file
>> "/Volumes/Main/Working/BIDS_TESTING/license.txt"
>>
>> Suggestions? How do I tell freesurfer where the license file is?
>>
>> Thanks so much,
>>
>> Dianne
>>
>>
>>
>> --
>> Dianne Patterson, Ph.D.
>> Research Scientist
>> d...@email.arizona.edu <d...@u.arizona.edu>
>> or
>> dianne...@gmail.com
>> University of Arizona
>> Speech and Hearing Science 314
>> 1131 E 2nd Street, Building #71
>> <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371=gmail=g>
>> (Just East of Harvill)
>> ==
>> If you don't hear back from me (and you expected to),
>> I blame the University's new SPAM filter.
>> Please write to my gmail account.
>> ==
>> Antipiphany: That moment when you realize how little you actually know
>> ==
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "bids-discussion" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to bids-discussion+unsubscr...@googlegroups.com.
>> To post to this group, send email to bids-discuss...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/ms
>> gid/bids-discussion/CAGpV9FJdPWuk7Xw5yAYp-O6iV%3DDiZEcZfDkU8
>> Nzjnn41pEiwcA%40mail.gmail.com
>> <https://groups.google.com/d/msgid/bids-discussion/CAGpV9FJdPW
[Freesurfer] freesurfer bids app cannot find license file
After trying the example bids app (which worked fine), I am trying the
freesurfer bids app:
https://github.com/BIDS-Apps/freesurfer
I have built the docker container on my mac and I have the ds005 data
directory here and the license.txt which I requested from freesurfer. I
asked for a linux license (assuming the container contains linux and that
was the relevant fact).
dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
/Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset
/outputs participant --license_file "license.txt"
1: You should define 'SliceTiming' for this file. If you don't provide this
information slice time correction will not be possible. (code: 13 -
SLICE_TIMING_NOT_DEFINED)
/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
/sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
/sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
/sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
/sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
/sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
/sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
/sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
... and 38 more files having this issue (Use --verbose to see them all).
Summary: Available Tasks: Available
Modalities:
133 Files, 1.77GBmixed-gambles taskT1w
16 - Subjects inplaneT2
1 - Sessionbold
Traceback (most recent call last):
File "/run.py", line 165, in
raise Exception("Provided license file does not exist")
*Exception: Provided license file does not exist*
===
If I provide the full path to the license file, it still fails:
docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
-v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset
/outputs participant --license_file "/Volumes/Main/Working/BIDS_
TESTING/license.txt"
Suggestions? How do I tell freesurfer where the license file is?
Thanks so much,
Dianne
--
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu <d...@u.arizona.edu>
or
dianne...@gmail.com
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==
Antipiphany: That moment when you realize how little you actually know
==
--
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu <d...@u.arizona.edu>
or
dianne...@gmail.com
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==
Antipiphany: That moment when you realize how little you actually know
==
___
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.
