Re: [Freesurfer] Recon-all

2022-05-05 Thread fsbuild 
External Email - Use Caution

Hello Krystally,
Try putting the directory Sub-132 under your userid’s home directory, i.e., 
/home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point 
to it. With the directory Sub-132 specified on your command line, you 
could then try,$ export SUBJECTS_DIR=/home/developer
- R.
On May 5, 2022, at 21:53, krystaly kryst...@hku.hk 
wrote:External Email - Use 
CautionDear Freesurfer 
experts,I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all 
command as demonstrated on the website (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html).Before
 running the command, I have converted DICOM files into NIFTI files. I, 
then, moved the nii files to Desktop at FS. They are in the folder named 
“Sub-132”. However, I got the following 
errors:developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s 
Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax 
error near unexpected token `('To make another attempt, I tried to 
process with another T1 image, and I got the following 
error:developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s 
Sub-132 -i Sub-132_T1_COR_5_0.5__250_i2.nii -allmkdir: cannot create 
directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission 
deniedmkdir: cannot create directory 
'/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot 
create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission 
deniedcp: cannot create regular file 
'/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such 
file or directorycat: 
/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such 
file or directoryINFO: FreeSurfer build stamps do not matchSubject 
Stamp:Current Stamp: 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt:
 No such file or directory.I reckoned that the T1 images could not be 
processed with only 1 plane. Would you please kindly advise on merging 
3-plane T1 images into one comprehensive T1-weighter image for further 
processing? Or would you please let me know what went wrong in this 
case?Thanks.Best 
regards,Krystal___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Recon-all

2022-05-05 Thread krystaly 
External Email - Use Caution

Dear Freesurfer experts,

I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as 
demonstrated on the website 
(https://secure-web.cisco.com/1UHVC1FSZYmyuNB9-Imz9busENdngVDz-sSAkkWD-mKGV9WnletKDmDav6XNh4DeufrnDsxlVSaMuIYqWMnp2hLM3OoPum_g7pP6r7ilayKRTXVKkLWOtldS6xNiyHXQfxvgCt2ouIPS3x05icPfPrnunp8pV6-x_Y36h3uUGIUqJG1UNdnKWioAtAuKXqMznQXSN7bza3kVliqHiLrq_py0C20DDvg8QgE1r3G6er-TK6ddpq77V4-sP1ET_Q9B5rvXkUnePAZOS1CrQxQ5HnCUZ2nWU25otZlabWPg6h8kvqC1D4Sdc_e1pI1HYOYRvTWDcoE6ZK3169cipg_2BFg/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_03_ReconAll.html).

Before running the command, I have converted DICOM files into NIFTI files.  I, 
then, moved the nii files to Desktop at FS.  They are in the folder named 
“Sub-132”.  However, I got the following errors:

developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i 
Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all
bash: syntax error near unexpected token `('

To make another attempt, I tried to process with another T1 image, and I got 
the following error:

developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i 
Sub-132_T1_COR_5_0.5__250_i2.nii -all
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': 
Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such 
file or directory
cat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No 
such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file 
or directory.

I reckoned that the T1 images could not be processed with only 1 plane.  Would 
you please kindly advise on merging 3-plane T1 images into one comprehensive 
T1-weighter image for further processing? Or would you please let me know what 
went wrong in this case?

Thanks.


Best regards,



Krystal


___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Passcode VM

2022-05-05 Thread fsbuild 
External Email - Use Caution

Sending the info to your email shortly.
- R.

On May 5, 2022, at 16:36, Marius Zeinhofer mari...@simula.no 
wrote:External Email - Use 
CautionHi,I am interested in 
the passcode for the VM as explained on the Freesurfer website.Thank you very 
much.Best,Marius___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Library Error

2022-05-05 Thread fsbuild 
External Email - Use Caution

Hello Jabeur,
Please check your setup. When the VM is first setup and run, there should 
be no library errors from freeview. You can test this with the following 
commands.
developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ 
pwd/home/developerdeveloper@developer-VirtualBox:~$ which 
freeview/usr/local/freesurfer/7.2.0/bin/freeviewdeveloper@developer-VirtualBox:~$
 ldd `which freeview` | grep "not 
found"developer@developer-VirtualBox:~$If you still see a library 
reported as not found then something happened with your environment and/or how 
freesurfer is now setup to cause the error. In that case, I recommend you 
delete the current FS_7_2_0_ubuntu_18_04_06 virtual machine from the VirtualBox 
client (choose to delete the files), setup the VM again, and when you first 
login check freeview again with the above commands.
When you want to process your own subject data we recommend you create a new 
directory in your home directory and set the environment variable SUBJECTS_DIR 
to point to it. The install of freesurfer including the provided subject 
data is meant for reference and the files are in a protected system directory. 
So it’s preferable to not modify and/or write files to where SUBJECTS_DIR 
points to out of the box. Instead, just create a new directory for 
processing subjects with, e.g.,

developer@developer-VirtualBox:~$ cd $HOMEdeveloper@developer-VirtualBox:~$ 
mkdir my_subjectsdeveloper@developer-VirtualBox:~$ export 
SUBJECTS_DIR=$HOME/my_subjects
- and put your subject data to process in $HOME/my_subjects
- R.
On May 5, 2022, at 19:14, Jabeur Mouna jabeurmo...@gmail.com 
wrote:External Email - Use 
Cautionimage.png___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

2022-05-05 Thread Joanna L Eckhardt 
External Email - Use Caution

Hi Paul,

Thank you so much for the timely response and the easy-to-follow explanation 
(and especially for the little tips on naming/spacing, which are helpful for a 
new coder). I did all these steps and everything worked great - the recon-all 
is running fine now.

Thank you!
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, May 5, 2022 1:26 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

Hi Joana,

There are a few things going on here.

First, you should create a subjects directory for FreeSurfer recons and tell 
FreeSurfer where it is by setting the SUBJECTS_DIR environment variable.  You 
should be able to do that with these 2 commands:

```
mkdir -p /home/developer/guest_shared/fs-subjects
export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects
```

Next, it looks like you've downloaded the dataset to a folder called 
`/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in 
the folder name are confusing recon-all.  Can you rename that directory and 
remove the spaces?  You should be able to do that in the file explorer, but 
this should also work:

```
mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' 
/home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/
```

You should then be able to run the recon-all command.  However, when running 
recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' 
(recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up 
session (ses-FU) in the dataset.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joanna L Eckhardt 

Sent: Thursday, May 5, 2022 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-All Error: "Command exited with non-zero status"


External Email - Use Caution

Hi FreeSurfer Team,

I am trying to run Recon-all on the cannabis test data on the freesurfer 
tutorial (I am running Ubuntu 18 VM on Windows os).

When I try to use the Recon-all command, I get the error "Command exited with 
non-zero status" and "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see

[Freesurfer] Library Error

2022-05-05 Thread Jabeur Mouna 
External Email - Use Caution

[image: image.png]
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] error estimates in FS total brain volumes

2022-05-05 Thread Alexopoulos, Dimitrios 
External Email - Use Caution

Hi all,

What is a reasonable estimate of the error margin in the total brain volume 
estimates of Freesurfer?

Is there a reference that discusses this?

Jim




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Curvature data question

2022-05-05 Thread Douglas N. Greve 
I re-ran your data and could not replicate. The only thing I can think 
is that you first ran the hires data at 1mm, then you reran with -hires. 
When I run from scratch with -hires, the data agree with the 1mm.
btw, I noticed that your 1mm was run with a development version of FS -- 
generally you should not do this.


On 5/4/2022 7:43 AM, Samuel Paré wrote:


External Email - Use Caution

Hi,

I apologize for the repeated emails, but I was wondering if you had 
the time to look at the 1mm data.


Sorry again and thank you so much,
Samuel

On Wed., Apr. 27, 2022, 11:03 a.m. Samuel Paré, 
 wrote:


No worries! Here are the 1mm results.

Thank you so so much for your help.
Have a great day,
Sam
B15mm1.zip



On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve
 wrote:

sorry, just looking at it now. Can you send the 1mm results as
well?

On 4/25/2022 7:42 PM, Samuel Paré wrote:


External Email - Use Caution

Hi,

I was wondering if you had new information on this matter.

Thank you very much,
Samuel

On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré
 wrote:

B15.zip


Hi Douglas,

Thank you again for your help. Here is one subject, let
me know if you need more.

Kind regards,
Samuel

On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve
 wrote:

That's so weird. Can you make the data available to us?

On 3/29/2022 8:00 AM, Samuel Paré wrote:


External Email - Use Caution

Hi Dough,

Thanks for your response. We followed your
suggestion and ran the 7T data without the -highres
option. This gave us values which are in the normal
range of what we get when using 3T mean curvature
data. We looked whether there was a fixed scaling
factor between the data with and without the
-highres option. This did not seem to be the case as
the scaling factor for the different subregions
varied between 1,18 (for the left G_subcallosal) and
2,95 (for the left S_collat_transv_ant). I attached
a pdf with the results.

Thank you again

On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve
 wrote:

This does not make sense to me. What resolution
is your 3T and 7T data? Can you run the 7T data
at 1mm (ie, without the -hires option) and see
if it changes?

On 3/20/2022 9:42 AM, Samuel Paré wrote:


External Email - Use Caution

Hello,

We are looking at some of our data acquired on
a 7T magnet. We ran recon-all with the
“highres” flag. The obtained results for
cortical thickness and cortical volume are very
comparable to data that we obtain when using 3
T brain images. However, the results for
cortical curvature are significantly different
from what we get by our 3 T data. I attach the
output of mean cortical curvature values using
the Destrieux atlas for a 3T and 7T dataset on
healthy controls. As you can notice, they
differ roughly by a factor of 2. Any
explanation for what may cause this large
difference?

Thanks,

Samuel


image.png
-- 
*Samuel Paré, MSc*

Laboratoire du développement et plasticité du

[Freesurfer] Passcode VM

2022-05-05 Thread Marius Zeinhofer 
External Email - Use Caution

 Hi,

I am interested in the passcode for the VM as explained on the Freesurfer
website.
Thank you very much.

Best,
Marius
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread Douglas N. Greve 
What does "isn't displaying the same i/j/k ras" mean? In what tool? What 
is the result of running mri_info on each volume?


On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

For some reason it isn't displaying the same i/j/k ras. The T1 and the 
registered image (ASL) is in the same dimension/voxel sizes. The TR is 
different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 
asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
falk.luesebr...@med.ovgu.de 

*Sent:* Thursday, May 5, 2022 4:17 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] Reversing mri_convert
    External Email - Use Caution

Hi Victor,


in case you used mri_convert like this only, there is no change in 
orientation or spacing between orig.mgz and T1.nii. So, whatever you 
registered to the T1.nii should also be in space of the orig.mgz.



Best,

Falk


...

[https://urldefense.com/v3/__http://secure-web.cisco.com/1bMxxPB2IQvUkA27JpoN6uYF_qZIvBhG7A1lEk_pEPVLjceSNqAuh2ELQrVXqmNwDxO-gqw8L1AEdbpyg24KUrplVS1nVMpzDvZMnLlMlxDizz858uiYsVJw3j_eJAy3F8ROeMbQQGdCNQdGmudIjjmSP-DmuF6zEpoivRhwTB0E-WM34a9y1lhuAPv-VfV01N0gdTr1Xu0mAeJ3pD89NxapxypjmT7CmixQuxq7DTT7jBhVsiWkIKPyDpRhTYXFDyhcmx2miIgf8JZXKyLUXTZiFip_eG0Rh9fS0KS7VC72MB4ubvSdGrS9rptNnBeE85QA02JCM-cayZ2SoocYUMw/http*3A*2F*2Fwww.med.ovgu.de*2Funimagdeburg_mm*2Fummd_focus.gif__;JSUlJSU!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZ3In85pA$ 
]

Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://urldefense.com/v3/__http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA/http*3A*2F*2Fwww.kneu.ovgu.de*2Fkneu.html__;JSUlJQ!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqaFxGR3sg$ 



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Zeng, Victor 
(BIDMC - Keshavan - Psychiatry) 

Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Reversing mri_convert


    External Email - Use Caution

Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move 
it back to Freesurfer space. How would you go about doing that? I am 
assuming I would do the inverse of the mri_convert, but I can't seem 
to find the option to write the matrix.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZWI937sQ$

Re: [Freesurfer] recon-all -long error (the third step of the longitudinal pipeline)

2022-05-05 Thread Douglas N. Greve 
What happens if you remove -parallel? That flag does not do much any 
more but cause trouble (we have removed it in recent versions)


On 5/3/2022 2:58 PM, FONG, manson CM [CBS] wrote:


External Email - Use Caution

Hello Experts,

I'm attempting to run the longitudinal pipeline, as described in this 
tutorial page (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial 
). 
I've tried the pipeline on 13 subjects (from the Alzheimer Disease 
Neuroimaging Initiative), each with varying number of time points. For 
all of them, I succeeded in the first two steps ( [CROSS] & [BASE] ), 
but recon-all threw an error for all subjects & for all time-points 
midway through the third step ( [LONG] ).


For example, for the subject 128_S_4832, I've run the cross-sectional 
step for all time points, resulting in corresponding folders called 
$SUBJECTS_DIR/128_S_4832_Ses01 and so on, and a template in the folder 
$SUBJECTS_DIR/128_S_4832 (from the [BASE] step). The exact command 
that exited with ERRORS was:


recon-all -long 128_S_4832_Ses01 128_S_4832 -all -parallel -openmp 16


Like in the first two step, I was using parallel computing with 16 
cores. From recon-all.log in the folder 
$SUBJECTS_DIR/128_S_4832_Ses01.long.128_S_4832/scripts, it appears 
that the last command that reported no issue was:


mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated


After this step, recon-all threw an error. The last four lines in my 
log file are:


Usage: reconbatchjobs logfile cmdfile1 [cmdfile2 ...]
See recon-all script for examples.
Linux ubda-d050 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7
19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 128_S_4832_Ses01.long.128_S_4832 exited with ERRORS
at Sat Apr 30 22:10:07 HKT 2022

I've searched the list and no similar errors have been reported.

1) FreeSurfer version: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

2) Platform: CentOS Linux 7 (Core)
3) recon-all.log & recon-all.error: see attached

Many thanks for your advice in advance!

Best regards,
Manson Fong


/Disclaimer:/

/This message (including any attachments) contains confidential 
information intended for a specific individual and purpose. If you are 
not the intended recipient, you should delete this message and notify 
the sender and The Hong Kong Polytechnic University (the University) 
immediately. Any disclosure, copying, or distribution of this message, 
or the taking of any action based on it, is strictly prohibited and 
may be unlawful./


/The University specifically denies any responsibility for the 
accuracy or quality of information obtained through University E-mail 
Facilities. Any views and opinions expressed are only those of the 
author(s) and do not necessarily represent those of the University and 
the University accepts no liability whatsoever for any losses or 
damages incurred or caused to any party as a result of the use of such 
information./



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] mri_surf2surf error

2022-05-05 Thread Douglas N. Greve 

what happens if you run
mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh

On 5/3/2022 11:54 AM, Zhang, Fan wrote:


External Email - Use Caution

Hello Everyone,


I am trying to run mri_surf2surf. But I got some errors saying "no 
such file or directory" while in fact there are files in the pathway. 
I was able to run this previously, so I am not sure if this is 
relevant to the recent upgrade of the Mac operation system (12.2.1). 
My FreeSurfer version is (Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does 
anyone know how to resolve this?



Thank you so much for the help!​


Fan




mri_surf2surf --hemi lh --s fsaverage5 --sval 
lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval 
lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh



sysnameDarwin

hostname Hans-iMac-Pro.local

machinex86_64

userfanzhang

srcsubject = fsaverage5

srcval= lh.CCn_band.Seed1_20220314.V1.13subjs.mgh

srctype=

trgsubject = fsaverage5

trgval= lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh

trgtype=

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

srchemi= lh

trghemi= lh

frame= 0

fwhm-in= 0

fwhm-out= 13

label-src= (null)

label-trg= (null)

OKToRevFaceOrder= 1

UseDualHemi = 0

Reading source surface reg 
/Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg


Loading source data

MRIallocSequence(0, 0, 0, 0): bad parm

No such file or directory

Segmentation fault: 11




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

2022-05-05 Thread Wighton, Paul 
Hi Joana,

There are a few things going on here.

First, you should create a subjects directory for FreeSurfer recons and tell 
FreeSurfer where it is by setting the SUBJECTS_DIR environment variable.  You 
should be able to do that with these 2 commands:

```
mkdir -p /home/developer/guest_shared/fs-subjects
export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects
```

Next, it looks like you've downloaded the dataset to a folder called 
`/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in 
the folder name are confusing recon-all.  Can you rename that directory and 
remove the spaces?  You should be able to do that in the file explorer, but 
this should also work:

```
mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' 
/home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/
```

You should then be able to run the recon-all command.  However, when running 
recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' 
(recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up 
session (ses-FU) in the dataset.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joanna L Eckhardt 

Sent: Thursday, May 5, 2022 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-All Error: "Command exited with non-zero status"


External Email - Use Caution

Hi FreeSurfer Team,

I am trying to run Recon-all on the cannabis test data on the freesurfer 
tutorial (I am running Ubuntu 18 VM on Windows os).

When I try to use the Recon-all command, I get the error "Command exited with 
non-zero status" and "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thank you!
Joanna

___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Recon-All Error: "Command exited with non-zero status"

2022-05-05 Thread Joanna L Eckhardt 
External Email - Use Caution

Hi FreeSurfer Team,

I am trying to run Recon-all on the cannabis test data on the freesurfer 
tutorial (I am running Ubuntu 18 VM on Windows os).

When I try to use the Recon-all command, I get the error "Command exited with 
non-zero status" and "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1nsoXu7DCJVVepnD_TI4lsupkcqto3lUNXVTynw-dkWgX0jgK5OMP6_Zvr1ZiIw5bdjvsH7QIZbXzwlVuvV8YaYPH31dXZld0PLKJQ6n6zVlT1vUWUcUvBjU9xD9Ofzw8OBKU4eRC_2DIyDBkLIBwF4vsHAAyJZ-hBJL7quyFxlQJ0salWFI5a5qUmD_AkXgyYHjsrbT5WlaGtqn-I72qhlbZm7rYYNqy2AO94040Acgj_3O1wejt1NmgePGUIMn08354kq_0lTEmwZFZX3GhybUyvRiTJq2YRAfWTZBVP9vbm7ve54riG7fhPUzP37cI/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


Thank you!
Joanna

___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] segmentHA_T1, mri_segstats: How can I get the PVC uptake for amygdalar nuclei?

2022-05-05 Thread Douglas N. Greve 
I don't think it is a good idea to try to PVC the amygdalar 
segmentations as they are too small.


On 4/28/2022 4:27 PM, Tun, Samantha wrote:


External Email - Use Caution

Hello Freesurfer Devs!

I am attempting to extract the tau uptake in the amygdalar 
segmentations. I ran this command:


mri_segstats --seg

rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i anat_resliced.mgz 
--sum


rHA_stats.dat

to try and calculate the tau uptake.

I was able to get an output, but I am unsure how to proceed from here. 
I basically want to get the pvc uptake of the amygdalar and 
hippocampal subfields scaled to the pons. I don’t think I can run the 
mri_gtmpvc command, so if you had any insight on how to calculate the 
scaled uptake of tau in the subfields, let me know!


Best,

Samantha


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Curvature data question

2022-05-05 Thread Douglas N. Greve 

not yet

On 5/4/2022 7:43 AM, Samuel Paré wrote:


External Email - Use Caution

Hi,

I apologize for the repeated emails, but I was wondering if you had 
the time to look at the 1mm data.


Sorry again and thank you so much,
Samuel

On Wed., Apr. 27, 2022, 11:03 a.m. Samuel Paré, 
 wrote:


No worries! Here are the 1mm results.

Thank you so so much for your help.
Have a great day,
Sam
B15mm1.zip



On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve
 wrote:

sorry, just looking at it now. Can you send the 1mm results as
well?

On 4/25/2022 7:42 PM, Samuel Paré wrote:


External Email - Use Caution

Hi,

I was wondering if you had new information on this matter.

Thank you very much,
Samuel

On Tue, Apr 5, 2022 at 9:04 AM Samuel Paré
 wrote:

B15.zip


Hi Douglas,

Thank you again for your help. Here is one subject, let
me know if you need more.

Kind regards,
Samuel

On Mon, Apr 4, 2022 at 10:40 AM Douglas N. Greve
 wrote:

That's so weird. Can you make the data available to us?

On 3/29/2022 8:00 AM, Samuel Paré wrote:


External Email - Use Caution

Hi Dough,

Thanks for your response. We followed your
suggestion and ran the 7T data without the -highres
option. This gave us values which are in the normal
range of what we get when using 3T mean curvature
data. We looked whether there was a fixed scaling
factor between the data with and without the
-highres option. This did not seem to be the case as
the scaling factor for the different subregions
varied between 1,18 (for the left G_subcallosal) and
2,95 (for the left S_collat_transv_ant). I attached
a pdf with the results.

Thank you again

On Sun, Mar 27, 2022 at 5:31 PM Douglas N. Greve
 wrote:

This does not make sense to me. What resolution
is your 3T and 7T data? Can you run the 7T data
at 1mm (ie, without the -hires option) and see
if it changes?

On 3/20/2022 9:42 AM, Samuel Paré wrote:


External Email - Use Caution

Hello,

We are looking at some of our data acquired on
a 7T magnet. We ran recon-all with the
“highres” flag. The obtained results for
cortical thickness and cortical volume are very
comparable to data that we obtain when using 3
T brain images. However, the results for
cortical curvature are significantly different
from what we get by our 3 T data. I attach the
output of mean cortical curvature values using
the Destrieux atlas for a 3T and 7T dataset on
healthy controls. As you can notice, they
differ roughly by a factor of 2. Any
explanation for what may cause this large
difference?

Thanks,

Samuel


image.png
-- 
*Samuel Paré, MSc*

Laboratoire du développement et plasticité du
système visuel
École d'optométrie
Université de Montréal



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has

Re: [Freesurfer] Scalable recon workflow

2022-05-05 Thread Douglas N. Greve 
btw, it will almost certainly be more efficient to run each subject with 
1 thread and run them all at the same time rather than running a few of 
them with 4 or 8. If you can run them all with multiple threads, then 
that might be more efficient (depends on your scheduler, for slurm it 
would be).


On 5/3/2022 3:57 PM, Wighton, Paul wrote:
There's a small percentage of subjects that need more than the 8Gb of 
memory (for mris_fix_topology if my memory is correct).


You could increase the memory allocation for all subjects, or you 
could run your entire dataset with 8Gb per subject, then re-run the 
ones that failed with increased memory.


-Paul

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Horn, Mitchell 
Jacob 

*Sent:* Tuesday, May 3, 2022 2:26 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Scalable recon workflow
Hi Paul,

Thanks for your speedy response! In that case, I assume 1GB/core is 
the memory allocation? Is it helpful to increase that?


Best,
Mitch

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Paul Wighton 


*Sent:* Tuesday, May 3, 2022 1:34 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Scalable recon workflow

External Email - Use Caution

Hi Mitch,

In our experience, -openmp 8 gives faster recons than -openmp 4, but 
the gains after -openmp 8 diminish quickly and aren't worth it.


-Paul

On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob 
 wrote:


Hi Experts,

If I have 100s of subjects to recon and have access to an HPC with
both GPU and CPU options what is the recommended flags to maximize
speed performance? Is … -parallel -openmp 4 … still the best
approach? And if so, is 2GB memory/core best (keeping it 8GB
memory/subject) or is there some better arrangement?

Best,

Mitch

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
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 Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline


<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

>
.
Please note that this e-mail is not secure (encrypted).  If you do
not wish to continue communication over unencrypted e-mail, please
notify the sender of this message immediately.  Continuing to send
or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to
communicate over unencrypted e-mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
External Email - Use Caution

Can I send three images so that you could debug? It is not seeming to work

Get Outlook for 
iOS

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Thursday, May 5, 2022 9:08:47 AM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Reversing mri_convert


If you have 2 volumes that share an RAS coordinate system but have different 
voxel geometry you can use the -rl (“reslice like”) option:



mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz



cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Zeng, Victor (BIDMC - 
Keshavan - Psychiatry)
Sent: Thursday, May 5, 2022 4:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Reversing mri_convert



External Email - Use Caution

Hi,



I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii



I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.



Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

--
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread Fischl, Bruce 
If you have 2 volumes that share an RAS coordinate system but have different 
voxel geometry you can use the -rl ("reslice like") option:

mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Zeng, Victor (BIDMC - 
Keshavan - Psychiatry)
Sent: Thursday, May 5, 2022 4:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Reversing mri_convert


External Email - Use Caution
Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
External Email - Use Caution

For some reason it isn't displaying the same i/j/k ras. The T1 and the 
registered image (ASL) is in the same dimension/voxel sizes. The TR is 
different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii 
asl.mgz, it doesn't change the incorrect i/j/k ras matrix

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
falk.luesebr...@med.ovgu.de 
Sent: Thursday, May 5, 2022 4:17 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [External] Re: [Freesurfer] Reversing mri_convert

External Email - Use Caution

Hi Victor,


in case you used mri_convert like this only, there is no change in orientation 
or spacing between orig.mgz and T1.nii. So, whatever you registered to the 
T1.nii should also be in space of the orig.mgz.


Best,

Falk


...

[https://secure-web.cisco.com/1OC7if2MmAqtO5LsFetXxMvabgQVMtCLToGm04c-ZSvPThev0LOfNk_G56d9kPe3hPRMffZ00a4QJALYUST-SlfOTC-IL34mMveIkE4P8GJ12aK0hUbXq4Rta0EgC7CxfRxzOplg4SrUAuWhSG7htFYK1i-YWM6lUA9y7M_4rb4i0RunJ0lDhDt3vWSzzyWdfq3gW4DtrEllcOuIs_zVrH8HA_Lf9Cu41F2PXbp05it7jzV0hey1DhPqdLfGVOAqr4OcJWB3slISuBy08jfGOiG0Mi5GQoJZnLjrC5ERQ01H4lMxPep0My4m87YwcQbcYpil2T9-jvFVyZ_ls1-LANQ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F1bMxxPB2IQvUkA27JpoN6uYF_qZIvBhG7A1lEk_pEPVLjceSNqAuh2ELQrVXqmNwDxO-gqw8L1AEdbpyg24KUrplVS1nVMpzDvZMnLlMlxDizz858uiYsVJw3j_eJAy3F8ROeMbQQGdCNQdGmudIjjmSP-DmuF6zEpoivRhwTB0E-WM34a9y1lhuAPv-VfV01N0gdTr1Xu0mAeJ3pD89NxapxypjmT7CmixQuxq7DTT7jBhVsiWkIKPyDpRhTYXFDyhcmx2miIgf8JZXKyLUXTZiFip_eG0Rh9fS0KS7VC72MB4ubvSdGrS9rptNnBeE85QA02JCM-cayZ2SoocYUMw%2Fhttp*3A*2F*2Fwww.med.ovgu.de*2Funimagdeburg_mm*2Fummd_focus.gif__;JSUlJSU!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZ3In85pA$
 ]
Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
https://secure-web.cisco.com/12VV1Zuktq-dOaOs2OFkciZgmD7fNFdt3i2XPDRjKwQTNpXi7umH4LgKS9BzXQqm6Vqij33b_wWWhN7Io1GIPT9jD5k1zNpB4namHa7EC7pULVlQI4RDilF5BjOb_KzR_ucPEcP7MWJjxRM16G0mzLt2H-VEGjo1CP4Dvkp4PIkr-dfwci8iP1qHMKKeBS9tuWOpMlCwwI4yBuofGhVj02VDTWrzngMl1EFs16kQqBeg0bQAwwEZEIt9ACyQEnPTRtzWibkAlg816zE3Z5RdZp_hkFkh33JCP6qBLoNPrCRmqKOE_xoWRRprs6WnXf22i2G62Kq0-V-WJ1g-vNsrnUw/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA%2Fhttp*3A*2F*2Fwww.kneu.ovgu.de*2Fkneu.html__;JSUlJQ!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqaFxGR3sg$

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Zeng, Victor (BIDMC - 
Keshavan - Psychiatry) 
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Reversing mri_convert


External Email - Use Caution

Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1td8aV2ri352TR9VpVlXrbsb7IaSAo2-icYdNvCin2ONbSEwqci7pGs9zwaGJF_Aq7E-W3dm2j1En6nCiuHq504nA_nPNbZzwM8_DgHT-0p9ll63KJ49_RbrhhbqpbjNly6fE0pYntN4JudpfCPRgnhM39VVfwfMoZVEjqix3SlAeS7QbNND0oe-gM4ATOvKb-TPGXjAPWrpwoisSaP6kL_hnYfeKBloe4h6RMenJL6IPNnRwyJapBkaM6CjnkaQEUMBLfiGSfuLb_oXFxjTo5gHplKiectEt8ObMQ1ZP4TEIeU2l9tuZZvJJjFI8zx6mRgfwWaocxws1zcufSAR15Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZWI937sQ$
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 Mass General Brigham 
Compliance HelpLine at

Re: [Freesurfer] Reversing mri_convert

2022-05-05 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Victor,


in case you used mri_convert like this only, there is no change in orientation 
or spacing between orig.mgz and T1.nii. So, whatever you registered to the 
T1.nii should also be in space of the orig.mgz.


Best,

Falk


...

[http://secure-web.cisco.com/1bMxxPB2IQvUkA27JpoN6uYF_qZIvBhG7A1lEk_pEPVLjceSNqAuh2ELQrVXqmNwDxO-gqw8L1AEdbpyg24KUrplVS1nVMpzDvZMnLlMlxDizz858uiYsVJw3j_eJAy3F8ROeMbQQGdCNQdGmudIjjmSP-DmuF6zEpoivRhwTB0E-WM34a9y1lhuAPv-VfV01N0gdTr1Xu0mAeJ3pD89NxapxypjmT7CmixQuxq7DTT7jBhVsiWkIKPyDpRhTYXFDyhcmx2miIgf8JZXKyLUXTZiFip_eG0Rh9fS0KS7VC72MB4ubvSdGrS9rptNnBeE85QA02JCM-cayZ2SoocYUMw/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif]
Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Zeng, Victor (BIDMC - 
Keshavan - Psychiatry) 
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Reversing mri_convert


External Email - Use Caution

Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Reversing mri_convert

2022-05-05 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
External Email - Use Caution

Hi,

I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii

I now have something registered to the T1.nii and would like to move it back to 
Freesurfer space. How would you go about doing that? I am assuming I would do 
the inverse of the mri_convert, but I can't seem to find the option to write 
the matrix.

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.