Re: [Freesurfer] Cannot find subject for recon-all

2023-05-12 Thread Pedro henrique barradas 
External Email - Use Caution

Thank you very much! It seemed to work but now it gives me another error message


Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJECTS_DIR/test1/01.nii -s 
$SUBJECTS_DIR/test1  -all

ERROR: You are trying to re-run an existing subject with (possibly)

 new input data (-i). If this is truly new input data, you should delete

 the subject folder and re-run, or specify a different subject name.

 If you are just continuing an analysis of an existing subject, then

 omit all -i flags.




De: freesurfer-boun...@nmr.mgh.harvard.edu 
 em nome de Huang, Yujing 

Enviado: segunda-feira, 1 de maio de 2023 18:20
Para: Freesurfer support list 
Assunto: Re: [Freesurfer] Cannot find subject for recon-all


External Email - Use Caution

Hi Pedro,



You need to provide full path to your .nii files.



You also need to set environment variable SUBJECTS_DIR to the directory you 
have write permission.



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pedro henrique barradas
Sent: Monday, May 1, 2023 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cannot find subject for recon-all



External Email - Use Caution



Hello!

I have recently installed freesurfer and was attempting to reconstruc some 
exams but I keep getting this error message



Pedros-Air:subjects pedrobarradas$ recon-all -i 01.nii. -s test1  -all

ERROR: cannot find 01.nii.



recon-all -s  exited with ERRORS at Mon May  1 16:51:37 WEST 2023



For more details, see the log file

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/1pYSnZbf72RgW-3ZCWzBOOst2BYZSSZ9N0Q_IzRh7Cvkr2ew0Ei8aSpA6SkbTItJFRlGX2uIEvmfmt6Qqdh2WBJhXKLBCo4c01hwN63_hEpNw6ocVeU6T-M3CzeV2iBdCpz9OBP2yboW-msmQEPYaxRBl5DVx9HEiYJBWB8rAfrYWrXhyIIxKa-qm4XAT3JTFba48cI_Vj5Ctfn_kIPoJcbIsm8pF8NZ6fAKOOeqyb6G8fcRmbGe3vMX-zYPpSpCyPyUNep8S5pOg8WKaaiJ-5P-FWB2jjWS3qExnwMDwhmRYya11UHRJgoPbvQkkqotVSE2fGgy84fp_9pKvek-frQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting





I'm not sure what I am doing wrong.

Any help would be tremendousy appreciated.



Best Wishes

Pedro Barradas
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[Freesurfer] [FreeSurfer] Process terminated when talairach was running

2023-05-12 Thread Krystal Xiwing Yau 
External Email - Use Caution

Dear FreeSurfer expoerts,


I am running recon-all for the subject on a HPC. It exited with error when 
talairach was running - it indicated "MINC_BIN_DIR: Undefined variable". The 
log file is attached to this email.


I tried to look up the directory, which contains MINC_BIN_DIR as indicated on 
the 

 forum 

 . When I type the command, there was none:


echo $MINC_BIN_DIR



Any advise would be highly appreciated. Lots of thanks.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Cannot find subject for recon-all

2023-05-12 Thread Huang, Yujing 
External Email - Use Caution

The message suggested subdirectory 'test1' already exists in your $SUBJECTS_DIR.

Pass a different subjid to -s <>, or delete directory 'test1'.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pedro henrique barradas
Sent: Friday, May 12, 2023 4:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cannot find subject for recon-all


External Email - Use Caution
Thank you very much! It seemed to work but now it gives me another error message


Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJECTS_DIR/test1/01.nii -s 
$SUBJECTS_DIR/test1  -all

ERROR: You are trying to re-run an existing subject with (possibly)

 new input data (-i). If this is truly new input data, you should delete

 the subject folder and re-run, or specify a different subject name.

 If you are just continuing an analysis of an existing subject, then

 omit all -i flags.




De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 em nome de Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Enviado: segunda-feira, 1 de maio de 2023 18:20
Para: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Assunto: Re: [Freesurfer] Cannot find subject for recon-all


External Email - Use Caution

Hi Pedro,



You need to provide full path to your .nii files.



You also need to set environment variable SUBJECTS_DIR to the directory you 
have write permission.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Pedro henrique barradas
Sent: Monday, May 1, 2023 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cannot find subject for recon-all



External Email - Use Caution



Hello!

I have recently installed freesurfer and was attempting to reconstruc some 
exams but I keep getting this error message



Pedros-Air:subjects pedrobarradas$ recon-all -i 01.nii. -s test1  -all

ERROR: cannot find 01.nii.



recon-all -s  exited with ERRORS at Mon May  1 16:51:37 WEST 2023



For more details, see the log file

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/1hYYBNnE0zViHLTfpy8vlUPODh2mEWusrsXcrii0Ua57OWj3rej3i7KKrQ_9MBI1ajI7gPXk5KFgiEBQ5Ka0NiOUGTSmL-ZkqM-4pDL48fg10CUQdoHNtNED0tw6sLAerbTcCJ8GrCNnqVcZ0gdJIxWAYxtqWIdXjlHOmj0jck5RlEIJksxEnXrwJ65FYqVhHPoU8qYz-J4cQzVLsUwieiD979nEESfA7RhJfnwEovXveCT9RXEUFCT_QXy7JTSSVkyuvX6QLDRv2qw0M8qOXMg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting





I'm not sure what I am doing wrong.

Any help would be tremendousy appreciated.



Best Wishes

Pedro Barradas
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Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

2023-05-12 Thread Douglas N. Greve 
   External Email - Use Caution

That's weird. In the echo below, is that from your shell or on the HCP? 
When you source the FS environment, that variable will be set.


On 5/12/2023 5:33 AM, Krystal Xiwing Yau wrote:


External Email - Use Caution

Dear FreeSurfer expoerts,


I am running recon-all for the subject on a HPC. It exited with error 
when talairach was running - it indicated "MINC_BIN_DIR: Undefined 
variable". The log file is attached to this email.



I tried to look up the directory, which contains MINC_BIN_DIR as 
indicated on the 
forum 
. 
When I type the command, there was none:



echo $MINC_BIN_DIR



Any advise would be highly appreciated. Lots of thanks.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong 
Kong.


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[Freesurfer] Password

2023-05-12 Thread m.77 ms77 
External Email - Use Caution

 I am attempting to use FreeSurfer on Windows via VirtualBox following this
tutorial:
https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWAMGVpkPu6bFqAMA5EdVLKSo3nlgdPLQ718QxJfiRlNrvYq1MHmKf_FWFd-MaSgcUY5axZCE83CscGWAh4OWO-XPLMxKxoCnPs0tAUJ4MzItyaP8aOirGHqqrGWSJy8P_C53Amuawevsk_cVo1-FK_AiYBJBOwv1FxpS1zGR37DtZDhJN7IUGJ9h3SfAr8X6-6iJAEtrfhVTUNBT4LTje-LPdRmkWIWgx4OASNaOa7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67_win
 <
https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWAMGVpkPu6bFqAMA5EdVLKSo3nlgdPLQ718QxJfiRlNrvYq1MHmKf_FWFd-MaSgcUY5axZCE83CscGWAh4OWO-XPLMxKxoCnPs0tAUJ4MzItyaP8aOirGHqqrGWSJy8P_C53Amuawevsk_cVo1-FK_AiYBJBOwv1FxpS1zGR37DtZDhJN7IUGJ9h3SfAr8X6-6iJAEtrfhVTUNBT4LTje-LPdRmkWIWgx4OASNaOa7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67_win
>Can I ask for the password that is required to log in Ubuntu when using
the  FS_7_2_0_Ubuntu_18_04_06.ova.7z

  provided in the tutorial?

Thank you very much
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[Freesurfer] recon-all for GM quantification

2023-05-12 Thread Nikolaidou, Sofia 
External Email - Use Caution

Good afternoon,

My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the 
DCC project. I am reaching out to ask for your advice on a FreeSurfer question.

I am using recon-all to try to quantify and compare GM volume and mean 
thickness among our subjects. In essence, I think I have all the necessary 
measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would 
you happen to know how I can customize the stream and reduce the processing 
time by taking out steps from the -all process? In other words, what would be 
the minimal set of steps that I have to run in order to acquire the above 
output files?

Thank you in advance!

Kindly,
Sofia


Sofia Nikolaidou | Clinical Research Coordinator
MGH/HST Martinos Center for Biomedical Imaging
149 13th St, Charlestown, MA 02129
Phone: 617-417-4463
snikolai...@mgh.harvard.edu
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Re: [Freesurfer] recon-all for GM quantification

2023-05-12 Thread Fischl, Bruce R.,PHD 
External Email - Use Caution

Hi Sofia

Unfortunately that doesn't really work as the most time-intensive steps are 
required. We are working on replacing some of these with deep-learning 
equivalents, but it will be some months before that is available.

Sorry
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nikolaidou, Sofia
Sent: Friday, May 12, 2023 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all for GM quantification


External Email - Use Caution
Good afternoon,

My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the 
DCC project. I am reaching out to ask for your advice on a FreeSurfer question.

I am using recon-all to try to quantify and compare GM volume and mean 
thickness among our subjects. In essence, I think I have all the necessary 
measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would 
you happen to know how I can customize the stream and reduce the processing 
time by taking out steps from the -all process? In other words, what would be 
the minimal set of steps that I have to run in order to acquire the above 
output files?


Thank you in advance!

Kindly,
Sofia


Sofia Nikolaidou | Clinical Research Coordinator
MGH/HST Martinos Center for Biomedical Imaging
149 13th St, Charlestown, MA 02129
Phone: 617-417-4463
snikolai...@mgh.harvard.edu
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[Freesurfer] password

2023-05-12 Thread m.77 ms77 
External Email - Use Caution

Sorry, I have a problem.
I am using FS_7_2_0_ubuntu_18_04_06.ova.7z on my virtual machine system but
it wants a password to open it.
What's the password of this file?
Thank's
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Re: [Freesurfer] EasyReg Troubleshoot - Killed

2023-05-12 Thread Iglesias Gonzalez, Juan E. 
External Email - Use Caution

Dear Nadia,
It seems like many centroids are missing. Did you visually check the 
segmentations of the reference and floating image, e.g., with Freeview? Do they 
look good?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nadia Kane 

Date: Wednesday, May 10, 2023 at 6:57 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] EasyReg Troubleshoot - Killed

External Email - Use Caution
Hi,
I increased the memory, and it ran partially to create the segmented input 
images, however I reached this error that I don't quite understand:

2023-05-10 17:16:15.526359: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not 
find cuda drivers on your machine, GPU will not be used.
2023-05-10 17:16:15.609260: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not 
find cuda drivers on your machine, GPU will not be used.
2023-05-10 17:16:18.907335: W 
tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not 
find TensorRT
using 1 thread
Segmentation of reference image already exists; reading from disk
Segmentation of floating image already exists; reading from disk
Linear registration
  Computing centroids and estimating affine transform
Traceback (most recent call last):
  File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 
1809, in 
main()
  File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 
194, in main
Mflo = getM(atlasCOG[:, ok > 0], floCOG[:, ok > 0])
  File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", line 
1198, in getM
x = np.matmul(np.linalg.inv(np.matmul(np.transpose(A), A)), 
np.matmul(np.transpose(A), b))
  File "<__array_function__ internals>", line 180, in inv
  File 
"/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py",
 line 552, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
  File 
"/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py",
 line 89, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix



Nadia Kane

Junior Imaging Specialist

University Imaging Centers | University of Minnesota
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On Tue, May 9, 2023 at 12:38 PM Nadia Kane 
mailto:kanex...@umn.edu>> wrote:
Hi,
I'm working on applying deep learning in image registration for a master's 
project. The overarching goal was to use real tissue clearing lightsheet data 
to perform the image registration, but first created some synthetically 
deformed brains based on the Allen Brain Atlas and Lab2im 
algorithm.
 However, I'm having some issues implementing the command in an Centos Linux 7 
(Core) HPC environment. The command gets Killed, I'm wondering if you could 
provide some more insight? Thank you!

I've set up my environment as follows:

module load mamba
mamba create -n freesurf # I named the environment freesurf
conda activate freesurf
mamba install tensorflow-gpu cuda-version=11.8


I've attached the easyreg.sh shell script that I run. Here's the output:

(freesurfer) kanex161@agc02 [~/Documents/Thesis/code] % bash easyreg.sh
2023-05-09 11:19:32.374206: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not 
find cuda drivers on your machine, GPU will not be used.
2023-05-09 11:19:32.405672: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not