Re: [Freesurfer] Freesurfer license

[Wighton, Paul]

Hi Liz,

Can you try adding a `-B ` to the `singularity 
run` command?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 2:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer license

Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this 
command:

singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4

I use this command to run fMRIprep:

singularity run --nv --cleanenv -B  -B   -B  -B   -w  --output-spaces 
{MNI152NLin2009cAsym:res-1,T1w:res-1} --ignore slicetiming --fs-license-file 
   
participant --participant_label  --skip-bids-validation

The only error I am getting is for the freesurfer license file location: 
--fs-license-file 

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html


thank you!!

L

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

Sent: Monday, June 3, 2024 12:33 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer license

Hi Liz,

What fmriprep container are you using and what are the full commands that are 
not working?

Are you bind-mounting the freesurfer license file into the container via 
`singularity exec --bind`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











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Re: [Freesurfer] Freesurfer license

[Wighton, Paul]

Hi Liz,

What fmriprep container are you using and what are the full commands that are 
not working?

Are you bind-mounting the freesurfer license file into the container via 
`singularity exec --bind`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ayoub, Lizbeth 

Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing 
the location of my freesurfer license ( it is a new license). I have tried all 
three options for location, and none work:

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked 
for an existing license file at several paths, in this order: 1) command line 
argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) 
the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at 
https://surfer.nmr.mgh.harvard.edu/registration.html

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











___
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] Freesurfer 7.3.1 MCR 2019b

[Wighton, Paul]

It looks like mris_compute_lgi won't work with *any* mcr and needs a full 
matlab installation.

Sorry :(

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Na, Xiaoxu 
Sent: Thursday, December 7, 2023 1:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution
Hi Paul,

Thank you so much for your confirmation! This is exactly what I’m having 
trouble with. In this case, maybe I can’t go with 7.3.1 and upper, I can go 
back to work with 7.1.1. Have you tried with 7.1.1 with mcrv84(matlab 2014b) 
running correctly? Last time I run LGI was on my own workstation with 7.1.0 and 
full matlab 2018b installed. Since I want to run all subjects on HPC this time, 
I have to build a docker to support that. If you have any version of 
freesurfer-mcr pair that is working for LGI, will you please kindly let me know 
and I’ll give it a try too? Thank you so much!


Regards,
Xiaoxu



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Thursday, December 7, 2023 11:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

I just tried this in a container. It looks like `mris_compute_lgi` is not 
designed to work with the mcr, and needs a full matlab installation. I started 
by jumping into a freesurfer 7. 3. 1 container. ``` docker run -it --rm 
freesurfer/freesurfer: 7. 3. 2
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I just tried this in a container.  It looks like `mris_compute_lgi` is not 
designed to work with the mcr, and needs a full matlab installation.



I started by jumping into a freesurfer 7.3.1 container.

```

docker run -it --rm freesurfer/freesurfer:7.3.2

```



Then I installed matlab mcr

```

fs_install_mcr R2019b

```



Note the output `fs_install_mcr` says:

```

On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:



/tmp/tmp.AzujBUG5W7/install-target/v97/runtime/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/bin/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/sys/os/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/extern/bin/glnxa64

```



But this is what should be added to the `LD_LIBRARY_PATH`:

```

export 
LD_LIBRARY_PATH=${FREESURFER_HOME}/MCRv97/runtime/glnxa64:${FREESURFER_HOME}/MCRv97/bin/glnxa64:${FREESURFER_HOME}/MCRv97/sys/os/glnxa64:${FREESURFER_HOME}/MCRv97/extern/bin/glnxa64:${LD_LIBRARY_PATH}

```



And I can confirm the `mris_compute_lgi` indeed does not work:

```

mris_compute_lgi --i $FREESURFER_HOME/subjects/bert/surf/lh.pial

ERROR: Matlab is required to run mris_compute_lgi!

```



But it looks like the mcr was installed:

```

find $FREESURFER_HOME/MCRv97

```



The error is a result of `getmatlab` not being able to find the matlab binary, 
which isn't included in the MCR.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://urldefense.com/v3/__https://github.com/freesurfer/freesurfer/blob/5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03/mris_compute_lgi/mris_compute_lgi*L56__;Iw!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA$<https://secure-web.cisco.com/1mYopLjr-lDIhMqYAqXF2VHCgLxTBzZfleAFg7ZLuPtenUy8m-FJ0KVOpf0ohKzuXa0PM16X6BLRIWEEQI2GAaRZPKAUyMXRzGUSYevad3oYqWzEcxs_obEHuL3FdSvJC4LMBAuTwNTQzMnO1n3Nb0YwdWtTjVpU5eCJ6fa0lTd4G8nJhBEzH7LVDCxkc7mughRdxr7zJlwnB33a_E1MYnWoTL4TzjKIVRJGl6E59M2D7sbio7tqySiofNC5a4cEaTXaMv4epFq5UW20WfwofMsAfyD1KUagZ15d9P7VsHbV1F_JfC4NdeCr_olYxxUCc/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03%2Fmris_compute_lgi%2Fmris_compute_lgi%2AL56__%3BIw%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA%24>



The `getmatlab` script:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://urldefense.com/v3/__https://github.com/freesurfer/freesurfer/blob/dev/fsfast/bin/getmatlab__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg$<https://secure-web.cisco.com/1iNn3UfSzhaLRI-ytx34ot5LUf_9_o6epLcaHVHfPyUkcpaoWz7o3NWK7CrzfMOuamuLMhlTzb4YuDmGv0wiGNXydK-QnYr8rjPcD4s9JBY5cC_KNwoocXV_fK0m487N2l2XR4qx_pbHqL0ow-dSNmmYYzgVSNwXL4QPcqfvTfm6bbcf2l9S2lQdHAU_4udFIGOwIzCtwCdqUB7dnhh4MshqJpFav0oYbCVwv4Oosdbo1md0qKf4d48vpJdKGoxCaL6cHa1lKnL072kxi1seMwjTMguWxJsQ0ys9LfY3W6ZsMGXt3TBi_g26cYJCTlJ05/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Ffsfast%2Fbin%2Fgetmatlab__%3B%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg%24>



-Paul





From: 
freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

[Wighton, Paul]

I just tried this in a container.  It looks like `mris_compute_lgi` is not 
designed to work with the mcr, and needs a full matlab installation.

I started by jumping into a freesurfer 7.3.1 container.
```
docker run -it --rm freesurfer/freesurfer:7.3.2
```

Then I installed matlab mcr
```
fs_install_mcr R2019b
```

Note the output `fs_install_mcr` says:
```
On the target computer, append the following to your LD_LIBRARY_PATH 
environment variable:

/tmp/tmp.AzujBUG5W7/install-target/v97/runtime/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/bin/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/sys/os/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/extern/bin/glnxa64
```

But this is what should be added to the `LD_LIBRARY_PATH`:
```
export 
LD_LIBRARY_PATH=${FREESURFER_HOME}/MCRv97/runtime/glnxa64:${FREESURFER_HOME}/MCRv97/bin/glnxa64:${FREESURFER_HOME}/MCRv97/sys/os/glnxa64:${FREESURFER_HOME}/MCRv97/extern/bin/glnxa64:${LD_LIBRARY_PATH}
```

And I can confirm the `mris_compute_lgi` indeed does not work:
```
mris_compute_lgi --i $FREESURFER_HOME/subjects/bert/surf/lh.pial
ERROR: Matlab is required to run mris_compute_lgi!
```

But it looks like the mcr was installed:
```
find $FREESURFER_HOME/MCRv97
```

The error is a result of `getmatlab` not being able to find the matlab binary, 
which isn't included in the MCR.
https://github.com/freesurfer/freesurfer/blob/5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03/mris_compute_lgi/mris_compute_lgi#L56

The `getmatlab` script:
https://github.com/freesurfer/freesurfer/blob/dev/fsfast/bin/getmatlab

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Na, Xiaoxu 
Sent: Thursday, December 7, 2023 12:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution
Thank you Paul! But I have already updated my neurodocker to the latest. I’ve 
tried to create a link using the same way you’ve listed below, and it didn’t 
help. In this way, I feel the mcr was not fully installed as I couldn’t locate 
the file MCRv97/bin/glnxa64/libmwlaunchermain.so, that’s why I turned to the 
official way, which installed a lot more files in that directory, but still not 
working.

The official way that R suggested, I feel like the script fs_install_mcr has 
already remove the temp it created during the installation once exit, so 
appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so 
much!


Regards,
Xiaoxu

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Thursday, December 7, 2023 10:35 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

Hi Xiaoxu, This is how I built a FreeSurfer 7. 1. 1 container with matlabmcr 
2014b (https: //urldefense. com/v3/__https: //github. 
com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min. 
md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$)
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Hi Xiaoxu,



This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b

(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://urldefense.com/v3/__https://github.com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min.md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$<https://secure-web.cisco.com/1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Fpwighton%2Ffs-docker%2Fblob%2Fmaster%2Fnotes%2F20201127-fs711-neurodocker-min.md%2Afreesurfer711__%3BIw%21%21LFqOYw%21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g%24>)



```

neurodocker generate docker \

  --base continuumio/miniconda:4.7.12 \

  --pkg-manager apt \

  --freesurfer version=7.1.1 \

  --matlabmcr version=2014b install_path=/opt/MCRv84 \

  --run "ln -s /opt/MCRv84/v84 /opt/freesurfer-7.1.1/MCRv84" \

| docker build -t pwighton/freesurfer:7.1.1 -

```



I had to create a symlink from /opt/freesurfer-7.1.1/MCRv84 to /opt/MCRv84/v84



You could try to see if 7.3.1 works with matlabmcr 2014b, or update the symlink 
accordingly for 2019b.



Hope this helps!



-Paul



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Na, Xiaoxu 

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

[Wighton, Paul]

Hi Xiaoxu,

This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b
(https://github.com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min.md#freesurfer711)

```
neurodocker generate docker \
  --base continuumio/miniconda:4.7.12 \
  --pkg-manager apt \
  --freesurfer version=7.1.1 \
  --matlabmcr version=2014b install_path=/opt/MCRv84 \
  --run "ln -s /opt/MCRv84/v84 /opt/freesurfer-7.1.1/MCRv84" \
| docker build -t pwighton/freesurfer:7.1.1 -
```

I had to create a symlink from /opt/freesurfer-7.1.1/MCRv84 to /opt/MCRv84/v84

You could try to see if 7.3.1 works with matlabmcr 2014b, or update the symlink 
accordingly for 2019b.

Hope this helps!

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Na, Xiaoxu 
Sent: Thursday, December 7, 2023 11:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution

Thank you for your information! However, even though I appended the temporary 
paths that were generated right after running mcr installation. While running, 
I first printed out the $ LD_LIBRARY_PATH, it seems right. However, the same 
error occurred. I didn’t install the freesurfer in the default folder, if that 
may be a problem. I used neurodocker to build the base image with freesurfer 
7.3.1 running correctly. Is there anything else I can try? Thank you so much!


Regards,
Xiaoxu


:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/usr/lib/x86_64-linux-gnu/:opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/tmp/tmp.s91tLX1Jfv/install-target/v84/runtime/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/bin/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/sys/os/glnxa64::/.singularity.d/libs
recon-all -s BL-101 -localGI
fs-check-version --s BL-101 --o /tmp/tmp.UQALDw
Thu Dec  7 15:57:37 UTC 2023

setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str
cd /home/xna/fmri/data_BF_str
/opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.UQALDw
-rwxrwxr-x 1 root root 18565 Dec  7 15:31 
/opt/freesurfer-7.3.1/bin/fs-check-version

freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
$Id$
Linux xbt090 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux
pid 107005
Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt
Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str
Actual FREESURFER_HOME /opt/freesurfer-7.3.1
-rw-rw-r-- 1 xna xna 1220527 Dec  7 13:57 
/home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log
Linux xbt090 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux
~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101
~/fmri/data_BF_str/BL-101
#@# white curv lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# white curv rh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Thu Dec  7 15:57:43 UTC 2023
cd /home/xna/fmri/data_BF_str/BL-101/mri

Re: [Freesurfer] Question about Freesurfer

[Wighton, Paul]

Hi Mahdi,

I'm afraid I don't know what you mean by "Freeview opens fine but when I load a 
column in it just shows a black view."  What is a column in this context?

As for registration between PET and MR, have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer

It suggests using mri_coreg.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mahdi Babaei 

Sent: Sunday, November 5, 2023 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question about Freesurfer

External Email - Use Caution

Dear FreeSurfer Team,

I'm currently a PhD student at Stevens Institute of Technology in New Jersey, 
USA, where my research focuses on MRI to PET translation. I have a number of 
problems. Freeview opens fine but when I load a column in it just shows a black 
view. Have you ever encountered this problem?
I'm so confused about using the tool for registration. Can I do registration 
between MRI and PET modalities of the same subject using "bbregister"?

Best,
Mahdi

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Re: [Freesurfer] Finding Intracranial volume

[Wighton, Paul]

Hi Peter,

recon-all produces an estimate of ICV.   In aseg.stats there is a line that 
looks like:

# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial 
Volume, 1696008.240403, mm^3

You can read more about how it is computed at
https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirsol Choi 

Sent: Wednesday, November 1, 2023 5:23 PM
To: Freesurfer support list
Subject: [Freesurfer] Finding Intracranial volume

External Email - Use Caution

Hi fellow freesurfers!

I am a Masters student currently working with diffusion images.

I would like to ask you experts how I can obtain ICV from my T1/T2 or diffusion 
images.

Is there a certain output from recon-all that produces intracranial volume? Or 
is there a different command I must use?

Thank you all so much for your time. I look forward to hearing from you.

Peter

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Re: [Freesurfer] Free surfer quits unexpectedly

[Wighton, Paul]

External Email - Use Caution

Thanks for this, R!

Monika (cc'd) is running into the same issue, and has followed these steps, and 
can now open files from the command line, but not from the GUI.

Any ideas?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Wednesday, October 4, 2023 1:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: c.massaneda_tu...@blackdog.org.au
Subject: Re: [Freesurfer] Free surfer quits unexpectedly

External Email - Use Caution


Please try the following,

… open a new terminal and run the bash shell … I am cd’d to /tmp though it 
should not matter ...

$ cd /tmp
$ bash
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit 
https://secure-web.cisco.com/1XuliApJYrA-3P4_QBQ0GnFFZuHT9GMh6g4UxP74WB2qI3NzvDV09_1m2EdDCmiBLP8S1rWen0y5sMkVn5wgT9n8RnT442f8dmc_5kGp4aq7-_SPfF3odvjGkWofk5q-sM3k3bJgMpSgAfZv5UWyXjDgwtTmPr8iiPKMxwlxE7w1bsKw51VApSkuPVymCKwFAgZr6rJ2WfrePNJjUvzuidjfZQENN6_MN0hvq4EGfvp3gQm106xQcpGiYQywaPu50/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050

… check the version of Quartz by starting an xterm..  When the xterm window 
opens check the version from the upper left hand corner XQuartz application 
pull down menu and check what “About X11” reports.  Check you have Quartz 2.8.2 
or later and then quit the xterm window.

Mac:/tmp> which xterm
/opt/X11/bin/xterm
Mac:/tmp> xterm &

… copy your license.txt file into your home directory.  For example if you 
downloaded the license by default into your Downloads folder, then copy it from 
there into $HOME …

Mac:/tmp> cd $HOME
Mac:~> cp -p -f ./Downloads/license.txt .

… set the environment variable FS_LICENSE to point to the license file … later 
you can put this in your shell init file to be the default when you launch a 
new terminal window with your default shell …

Mac:~> export FS_LICENSE=$HOME/license.txt
Mac:~> head -1 $FS_LICENSE
y...@somedomain.com   <— email you used to register for the 
license

… setup the freesurfer environment …

Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1
Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME   /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR   /Applications/freesurfer/7.4.1/mni

… first check freeview with no arguments opens an empty window …

Mac:~>  which freeview
/Applications/freesurfer/7.4.1/bin/freeview
Mac:~> freeview

… close the freeview window and try to open a knoen to be good volume file ...

… check the volume file exists …

Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz
-rwxr-xr-x  1 root  wheel  4502402 Jul 13  2021 
/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz*

… try opening the volume file …
Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz

If the above works try opening one of your own volume or surface files.

BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are 
important security fixes in 12.7.

- R.

On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu 
 wrote:


External Email - Use Caution

Hi,

I'm attempting to install and run FreeSurfer, but every time I try to load 
data, the program unexpectedly quits. I downloaded the license from the email 
sent by FreeSurfer and followed the instructions of the video tutorial.

I've also downloaded and installed the latest version of XQuartz before 
installing and executing FreeSurfer.. When I tried to open FreeView in my 
terminal and load the image, there was no message in my terminal explaining why 
the program crashes.

The version of FreeSurfer that I'm using is 
freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running 
version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of 
memory.

I've searched the list, and no similar errors have been reported. Does anyone 
have any thoughts on how to troubleshoot this issue?

Thanks for your help.


Clara MT
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Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged

[Wighton, Paul]

External Email - Use Caution

Hey Sebastien,

I'm not sure how to do this in FreeSurfer (mri_add_xform_to_header might work) 
but you can overwrite the header in python using nibable.  You'll have to 
compute the vox2ras yourself however.

Let's say you have image 1 and image 2 and you want to overwrite the header in 
image 2.  I would set the grad2ras matrix (what mri_info calls 'xform info') of 
image 2 to be what is in image 1, then use the voxel sizes of image 2 to 
compute the vox2ras from the grad2ras.

Here is some code (from the autoprescribe notebook!) showing how to go from 
vox2ras to grad2ras, you'll need to go in the opposite direction (grad2ras --> 
vox2ras)

```
# Given
#   - A nibable img as returned by nb.load()
# Compute
#   - The vox2ras matrix (this is simply img.affine)
#   - The grad2ras matrix (mri_info calls this xform info)
#   - See mri.cpp:12818
def calc_transforms(img):
vox2ras = np.copy(img.affine)
grad2ras = np.copy(vox2ras)

# - pixdims is same as xsize, ysize, zsize in mri.cpp:12818 
# - c is same as c_r, c_a, c_s in mri.cpp:12818
# - use of 1:4 here is probably fragile
pixdims = img.header['pixdim'][1:4]
c = img.header['dim'][1:4] / 2

grad2ras[0:3,0:3] = vox2ras[0:3,0:3] / pixdims
grad2ras[0:3,3]   = vox2ras[0:3,3]   + vox2ras[0:3,0:3] @ c

return vox2ras, grad2ras
```

Good luck,

-Paul



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Proulx, Jean Sebastien 

Sent: Friday, September 8, 2023 9:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Copy geometry (fov position) from one header to 
another while keeping voxel and matrix sizes unchanged

External Email - Use Caution
Dear Freesurfers,

Any chance anyone has a suggestion to achieve that? I’m a bit stuck.

Summary: two runs of a single-slice image don’t aligned in RAS space, but they 
do in brain space (at the scanner, the head moved between the runs but the FOV 
was adjusted accordingly with autoalign-like routine). The two runs have 
different voxel and matrix sizes. I want to copy the geometry information from 
one run to the other without resampling the data, so that the two can be 
properly overlayed in freeview. mri_convert with the --in_like flag does not 
work with unmatched voxel grids.

Thanks for you help and
Have a great day!
Sebastien

From: Proulx, Jean Sebastien 
Date: Monday, August 28, 2023 at 3:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: RE: Copy geometry (fov position) from one header to another while 
keeping voxel and matrix sizes unchanged
Exactly, the two runs align in voxel space but not in RAS space.
mri_convert with the --in_like did the trick, thank you very much.

Now I have another scenario where the two runs also don’t align in RAS space 
but where they would align in voxel space if they had the same voxel grid 
dimensions (the second run has twice the spatial resolution). I need to achieve 
the same thing: adjust geometry in the header of the second run—without 
changing the data—so it aligns in RAS space with the first run.

mri_convert with --in_like unfortunately complains for that second scenario:
“error: volume sizes do not match”

Thanks again a lot for your help and
Have a great day!
Sébastien

From: Greve, Douglas N.,Ph.D. 
Sent: Monday, August 28, 2023 10:47 AM
To: Proulx, Jean Sebastien ; 
freesurfer@nmr.mgh.harvard.edu
Subject: Re: Copy geometry (fov position) from one header to another while 
keeping voxel and matrix sizes unchanged

To confirm, the two volumes *without any transformation (ie, "untouched")* do 
not align in FV but they do align in fslview? In other words, they align in 
voxel space but not in RAS space?
To just copy the geometry, run
mri_convert run2.nii.gz --in_like run1.nii.gz run2-in-run1.nii.gz


On 8/28/2023 10:10 AM, Proulx, Jean Sebastien wrote:
Sorry for sending to the wrong place, will do in the future. Here it is.

Thanks for the suggestion! The two fov indeed don't align in freeview. I played 
a little with the --no-resample option but did not acheive what I wanted.

Here I simplified the problem to two single-slice images (run1.nii.gz and 
run2.nii.gz attached) acquired the same way (same resolution) but in two 
different positions in scanner space. In freeview it looks like this:
freeview anat.nii.gz run1.nii.gz run4.nii.gz
[Image]

I need the fov to align, but the data to not change at all (because the fov 
moved with the patient's head during the experiment).

To get the transformation, I ran
tkregister2 --mov run4.nii.gz --targ run1.nii.gz --regheader --reg run4to1
and clicked "save reg" without touching anything. It spits out the following 
matrix
 0.99988  -0.01117   0.01053  -0.63259;
 0.01065   0.99879   0.04792  -0.70029;
-0.01105  -0.04780   0.99880  -3.93196;
 0.0   0.0   0.0   1.0;
Is this indeed the run4 to run1 transformation matrix? Do you know of a way to 
get that 

Re: [Freesurfer] PetSurfer, PET data format, mri_convert

[Wighton, Paul]

External Email - Use Caution

Hi Zeyu,

It looks like your files are in 'interfile' format.

If you have access to pmod, you might be able to use that to convert your files 
to nifti.
https://secure-web.cisco.com/1zqVVdVIc7totHjAN-r1V2oHpo0YeUbAKoFLyEzf5hGF_2QpNKUkYjapa61k7l3PSjeARv8qdfQNsmsWgyLM_x7yRo7uvps9iIp9uwO7a2TINpqT1lUcfZcSARBl8Fns-rGgqjVdinmxYTRRJW7qEhjB7TFy_Akeg1X6PozmQwtUClLKAap1CgLy0N6P-i1td6Epv8GJIS-_NewalfMvYf-uyOe7TemfME6k238__pKMda6B1y1hwLdR5PEBewmHUOTI5Z0xkuVuplriFkvuAaw/https%3A%2F%2Fwww.pmod.com%2Ffiles%2Fdownload%2Fv31%2Fdoc%2Fpbas%2F684.htm%23%3A%7E%3Atext%3DInterfile%2520is%2520a%2520file%2520format,version%203.3%2C%20Nucl%20Med%20Commun.

Or you could try using this: 
https://secure-web.cisco.com/1V87W-pEHHar2tKNTfSutV2rBhxv4QVhkEBhm-a5RZ9q6Gz-7E2XdigrjJkwDqcX7klh7tFuRWLL-91eC6kvPzjRRqZhQnS5wwjEH2gT566KrsPTsUSgBpXi1HnBlucbgC5JunCkl-6FVnKsvzu3cCbBMp82g0-NeCBdJM_xFIERvYEYDp6ArkE6kKJ18zQhGHc3KX4095fGBoZgt7_PI5_RP7B5AEA-HCHemz72hJe_7FTpJkw6Giy3l28FBafW09nazM9MZx3-XJ1nWYzDVRA/https%3A%2F%2Fgithub.com%2Frordenlab%2Fi2nii

Good luck!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zhou, Zeyu 

Sent: Friday, July 28, 2023 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] PetSurfer, PET data format, mri_convert

External Email - Use Caution

Hi Freesurfer developers,

I am new to PET and FreeSurfer. I am trying to go through the PetSurfer 
tutorial (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1WIdRjlXspzVNAAubGnxONoOi-JQqlKFaZgFpmpGW_4cj_NGoWMbZCmxAW1Lx2XUGPrto07cKnoNmWSMabwUBhdizuJ3mimj9Xd_MWpUSafdFT4ojOiEHnwrT0iBPizzRaKXMlYsvKENtDO5ccRa8UEo9gWeMyQ0bNS2k2tUOQgdDchNUPKBRvJq54IaFi4y0eKS3ZSLgf78xNoL7Ng6qOqEMXMWX71tcHgARz3rerCE6795uAmZuqzjgij7h-thEDV9w3pPcJD-2qnuXbJpekQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 In Part 4 "Reg
 ister your PET image with the anatomical", the PET data format in example is 
.nii.gz. However, here are the PET data I have (collected from SIEMENS HRRT 
PET):

309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr

I tried converting the .i file to (for example) an .nii file by mri_convert but 
got the following error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii
ERROR: cannot determine file type for 
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i

Then I changed the .i file's extension to .img and the .i.hdr file's extension 
to .hdr and run mri_convert, but still got an error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii
reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img...
error: ReadAnalyzeHeader: unsupported data type 17741

I couldn't find anywhere about how to process PET data in .i and .i.hdr files. 
Any suggestions? I attached one .i.hdr file for your reference.


1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Ventura 13.4.1 (c)
3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  
8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64


Thanks.

Best,
Zeyu Zhou


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 .
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Re: [Freesurfer] apply an existing linear transform to a GRE phase map

[Wighton, Paul]

External Email - Use Caution

Hi Daniel,

It's been a while since I looked into this, but I think you'll need to use 
`lta_convert` to convert your lta to xfm format, then use 
`mri_add_xform_to_header` to overwrite the header of your phase map.

You might have to extract the current transform from your phase map, apply the 
robust_regsiter transformation then write the resulting xfm back to your phase 
map file.

There is also mri_convert which has an `--apply_transform` flag, but I think 
that resamples the data.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Balentine, Daniel Grimm 

Sent: Wednesday, May 3, 2023 4:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] apply an existing linear transform to a GRE phase map

External Email - Use Caution
Hello FreeSurfer Developers,

I hope you are well. I’m attempting to apply an .lta file generated by 
mri_robust register. The files I want to apply the transform on are GRE phase 
maps, so I don’t want to do any resampling.

I was looking around mri_vol2vol, but all the examples seem to involve 
resampling to a target scan. How would I go about this if I simple want to 
apply this linear transform on the phase maps (nii) in freesurfer?


  1.  Freesurfer version 7.3.0
  2.  Platform: CentOS Version 7

Sincerely,

Daniel Balentine

Data Analyst
Athinoula A Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 - 13th Street
Charlestown, MA 02129
dbalent...@mgh.harvard.edu



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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] FreeSurfer container recipe?

[Wighton, Paul]

Hi Bennet,

I've been doing my best to support building FreeSurfer containers via 
neurodocker (https://github.com/ReproNim/neurodocker).

This template should give you a good idea of the pre-reqs for a FreeSurfer 
container.
https://github.com/ReproNim/neurodocker/blob/master/neurodocker/templates/freesurfer.yaml

And you can also use neurodocker to install other required components like FSL, 
niftyreg, ants, etc.

I also have a PR in the works to support compiling FreeSurfer from source, but 
it's a mess right now and I haven't had time to clean it up.
https://github.com/ReproNim/neurodocker/pull/445

Hope this helps,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bennet Fauber 

Sent: Thursday, April 6, 2023 7:34 AM
To: Freesurfer support list
Subject: [Freesurfer] FreeSurfer container recipe?

External Email - Use Caution

In reply to mail from Mitchell Horn, Douglas Greve replied

> The math libraries changed between 7 and 8, nothing we can do about it. When I
> have to run things on a centos8 machine, I generally run in a centos7 
> singularity
> container (which we might be able to make available, without support:)

Would it be possible to get just the Singularity definition file for
the CentOS 7 Singularity image that you use posted to the FS wiki?

We're happy to do the building, but having a file that lists the
needed prerequisites that need to be installed via yum prior to
installing FreeSurfer would be very helpful.  It would also help to
see how you handle the needed FSL components, and I think at least
some portion of ANTs is needed for TRACULA, so even just which
binaries are needed would be a help, too..

Thanks for considering this request, which I hope is not as burdensome
as providing the fully built container.

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The information in this e-mail is intended only for the person to whom it is 
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Re: [Freesurfer] Flipping Thickness Matrices

[Wighton, Paul]

Hi Anam

Sorry for the lag.  mris_left_right_register takes as input surfaces, not the 
overlays or thicknesses.

To flip an overlay file, here is what I would do.  Maybe others can chime in on 
weather this makes sense or if there is an easier way.  

I'd start by running mris_left_right_register.  Then, I would use read_surf.m 
to load in the original, and registered surfaces, eg lh.right and 
lh.sphere.left_right.  Then, I would go through each vertex in lh.right and 
find the corresponding (or closest) vertex in lh.sphere.left_right.  This 
correspondence will define a mapping you could then apply to the overlays.

-Paul


From: Anam Anzak 
Sent: Wednesday, March 15, 2023 3:52 AM
To: Wighton, Paul; Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: Re: Flipping Thickness Matrices

External Email - Use Caution

Dear Paul,

Thank you for your reply! Just one thing we haven't really figured out... does 
mris_left_right_register take as input the thickness (mgh) files or the 
surfaces? I've been trying but can't really apply it to the thickness files. In 
theory, we would really just like to flip the thickness matrix right->left... 
is mris_left_right_register something we should apply upstream of the thickness 
file generation?

Thank you and all the best,
Bernardo and Anam

--
Bernardo Pimentel
Neurology Resident
Department of Neurology - Christian-Doppler University Hospital
Paracelsus Medical University
Salzburg, Austria

Miss Anam Anzak MBBS PhD MRCS PGCCE
NIHR Clinical Lecturer (Neurosurgery)
Specialty Registrar in Neurosurgery, London deanery

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

Sent: 07 March 2023 21:31
To: Freesurfer@nmr.mgh.harvard.edu 
Cc: Bernardo Pimentel 
Subject: Re: [Freesurfer] Flipping Thickness Matrices

Hi Anam,

Check out mris_left_right_register.  It's not super well documented, but it 
takes as input the right and left hemispheres, inflated onto a sphere, and 
outputs the left hemisphere registered to the right and the right hemisphere 
registered to the left, also inflated onto a sphere.

If you'd like to do this in matlab, perhaps looking at the code for 
mris_left_right_regsiter would help
https://github.com/freesurfer/freesurfer/blob/dev/mris_left_right_register/mris_left_right_register.cpp<https://secure-web.cisco.com/1IwEg4Ngb-r-J1t-vbpx7YHZQj0wpI3pm8yDOxlEsVPbG9aHMjST1Zv4dmfGDlKw8xL5o8GYkytU3ISu0F5HlXjONh2LzdtmgzKFJ0WwnLXHfA18XsLx4iMYbDiteSBCazkrtdTg7f25v5HZ7xfz8XNdZ7ka2CRQQqGNvMDf2EEHXqV2DNYIAL6pRWufQVVNmDXI1YuhcaLz27rpi_1yWgrPozQc5QxAxSi4KOTMLWdE4wcAACPJhgG8TI2cXlEP0reXb7KKBFSpCJoJ1rb7NyeaNTztnK06U7f0rxM4ZY8ax2ZYJRPjygatZbyMQ4pvA/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fmris_left_right_register%2Fmris_left_right_register.cpp>

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anam Anzak 

Sent: Tuesday, March 7, 2023 4:00 PM
To: Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: [Freesurfer] Flipping Thickness Matrices

External Email - Use Caution

Dear FreeSurfer Community,

Has anyone had any success with solving the below problem:

I am dealing with brain lesions which may present on the left or right 
hemisphere of the brain.


  1.  I wish to 'FLIP' RIGHT sided hemispheres (which contain lesions) to the 
LEFT side, so I ultimately can collate all my data and analyse brain 
hemispheres that are IPSILATERAL or CONTRALATERAL to the side of the brain 
lesion.
  2.  When I use the Flip function below, the matrix generated seems to be 
correct, HOWEVER the subsequent IMAGE generated from the matrix, appears 
incorrect (it is not at all a mirror image of the original image).
  3.  NOTE: My matrices include a Lesion Mask and a Medial Wall Mask (I am 
interested in examining Cortical Thickness values of all the cortex EXCEPT the 
lesion and medial wall (tentorium and ventricles etc).

Here are the commands used, for eg. 'subject 1':


%% 4b. Load the binary Lesion masks RIGHT


right_lesion_filelist= strcat(P, '/Oedema_masks_bin/', Imaging_Code, 
'_rh_fsaverage5_bin.mgh');


% load RIGHT lesion masks into a matrix

right_lesions   = SurfStatReadData([right_lesion_filelist]);
right_lesions = ~right_lesions;

% create a left hemisphere matrix filled with 1s
left_hemisphere = ones(17,10242)

% concatenate horizontally lesions masks (L) with right hemisphere matrix
fullbrain_with_right_lesions = horzcat(left_hemisphere, right_lesions)

% create medial wall mask for all subjects
r_whole_mask = repmat(mask, 17, 1)


% add the medial wall mask on the lesion masks

fullbrain_lesion_medialwall = fullbrain_with_right_lesions.*r_whole_mask

% apply matrix with lesion & medial wall to the thickness values
T_right = fullbrain_lesion_medialwall .* T_rightlesion

%% Flip the Right sided images to the left

% reverse the element in each

Re: [Freesurfer] Transparency issue in FreeView

[Wighton, Paul]

Great, thanks R!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Friday, March 17, 2023 1:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: anthony.gala...@nih.gov
Subject: Re: [Freesurfer] Transparency issue in FreeView

External Email - Use Caution

My guess is remote rendering via ssh uses a different set of drivers compared 
to rendering done sitting at the console of the CentOS8 machine.  Usually it is 
remote rendering that is broken more often than not because of differences in 
OpenGL drivers or the graphics card on the machine ssh’ing in receiving X11 
forwarding, e.g. OpenGL trying to work in headless mode.

Either way, you can try setting  LIBGL_DEBUG=verbose to see what’s reported 
and/or different between the local and remote environments.
$ export LIBGL_DEBUG=verbose
… or just on the command line when you run the command …
$ LIBGL_DEBUG=verbose  freeview 

Graphics card drivers from vendors like NVIDIA can modify system libGL 
libraries and some people have found that for (remote) rendering to work those 
drivers need to be uninstalled.  I have not heard of that adversely affecting 
rending from the host machine’s console however.  But you might want to check 
you have the latest OpenGL drivers installed on the CentOS8 machine, e.g., 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.linuxquestions.org/questions/linux-software-2/how-can-i-check-if-i-have-installed-opengl-on-my-centos-server-4175583741/<https://secure-web.cisco.com/1B4t-A6P6PLfb6I410WFHd2fC2dzFjhrrZdNQmE6UFLRRZJLnGjhrdu9AYNhUWe1nkLoVTgxqLkxcQHNp5BNwuu1xjnESn2j_vwW2AtpzOfFSQcypMrWDFDj3btA1P6VUPN91bhWihmdw2sC4i7424AtsZx75anykaHH3zdwypzBJRT9WnPL4TqHZ_EsQhXQ060kXRRe5mqzvDcCUTOPBoXz3UZKbEHOJuRyiOBwXWjY32fLztID94WznfZyRvWwSL8uBK7lhdkihldizusJzg7SYFHSJNDVwvTNd3WQusi1CNGbCBUrSIe1dEcdgxATHul0JJSWxAFrwm5UFJMbzpQ/https%3A%2F%2Fwww.linuxquestions.org%2Fquestions%2Flinux-software-2%2Fhow-can-i-check-if-i-have-installed-opengl-on-my-centos-server-4175583741%2F>

This article is more geared towards remote debugging, but might give you some 
insight, https://www.scm.com/doc/Installation/Remote_GUI.html

- R.

On Mar 16, 2023, at 19:19, Wighton, Paul  wrote:

Hi All,

I have a colleague who is trying to use FreeView on Red Hat Enterprise Linux 8, 
and there seems to be a transparency issue where windows behind the viewer are 
being displayed.  See attached screenshot.

This only happens when using FreeView on the desktop.  When using freeview over 
`ssh -X` everything looks good.

Any ideas, or debugging info we could pass along?

Thanks,

-Paul___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Flipping Thickness Matrices

[Wighton, Paul]

Hi Anam,

Check out mris_left_right_register.  It's not super well documented, but it 
takes as input the right and left hemispheres, inflated onto a sphere, and 
outputs the left hemisphere registered to the right and the right hemisphere 
registered to the left, also inflated onto a sphere.

If you'd like to do this in matlab, perhaps looking at the code for 
mris_left_right_regsiter would help
https://github.com/freesurfer/freesurfer/blob/dev/mris_left_right_register/mris_left_right_register.cpp

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anam Anzak 

Sent: Tuesday, March 7, 2023 4:00 PM
To: Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: [Freesurfer] Flipping Thickness Matrices

External Email - Use Caution

Dear FreeSurfer Community,

Has anyone had any success with solving the below problem:

I am dealing with brain lesions which may present on the left or right 
hemisphere of the brain.


  1.  I wish to 'FLIP' RIGHT sided hemispheres (which contain lesions) to the 
LEFT side, so I ultimately can collate all my data and analyse brain 
hemispheres that are IPSILATERAL or CONTRALATERAL to the side of the brain 
lesion.
  2.  When I use the Flip function below, the matrix generated seems to be 
correct, HOWEVER the subsequent IMAGE generated from the matrix, appears 
incorrect (it is not at all a mirror image of the original image).
  3.  NOTE: My matrices include a Lesion Mask and a Medial Wall Mask (I am 
interested in examining Cortical Thickness values of all the cortex EXCEPT the 
lesion and medial wall (tentorium and ventricles etc).

Here are the commands used, for eg. 'subject 1':


%% 4b. Load the binary Lesion masks RIGHT


right_lesion_filelist= strcat(P, '/Oedema_masks_bin/', Imaging_Code, 
'_rh_fsaverage5_bin.mgh');


% load RIGHT lesion masks into a matrix

right_lesions   = SurfStatReadData([right_lesion_filelist]);
right_lesions = ~right_lesions;

% create a left hemisphere matrix filled with 1s
left_hemisphere = ones(17,10242)

% concatenate horizontally lesions masks (L) with right hemisphere matrix
fullbrain_with_right_lesions = horzcat(left_hemisphere, right_lesions)

% create medial wall mask for all subjects
r_whole_mask = repmat(mask, 17, 1)


% add the medial wall mask on the lesion masks

fullbrain_lesion_medialwall = fullbrain_with_right_lesions.*r_whole_mask

% apply matrix with lesion & medial wall to the thickness values
T_right = fullbrain_lesion_medialwall .* T_rightlesion

%% Flip the Right sided images to the left

% reverse the element in each row
subject1 = T_right(1,:)

SurfStatView(subject1, SP)

SP = SurfStatAvSurf({[P '/fsaverage5/surf/rh.pial'],[P 
'/fsaverage5/surf/lh.pial']})
subject1_flipped = fliplr(subject1)
SurfStatView(subject1_flipped, SP)

mirror_image = fliplr(T_right)

SurfStatView(mirror_image(1,:), SP)


Any thoughts would be very much appreciated!
Kind regards
Anam


Miss Anam Anzak MBBS PhD MRCS PGCCE
NIHR Clinical Lecturer (Neurosurgery)
Specialty Registrar in Neurosurgery, London deanery

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 .
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] Failing to execute QDEC

[Wighton, Paul]

Hi Vittal,

I tested your license file and it's fine.  Are you sure it's in the right 
place?  What's the output of `cat /usr/local/freesurfer/license.txt`?

It also looks like QDEC is trying to write to 
`/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have 
permissions to write there?  I'd suggest creating a FreeSurfer subjects 
directory under your home and setting the SUBJECTS_DIR environment variable 
accordingly, e.g.

mkdir ~/fs-subjects
export SUBJECTS_DIR="${HOME}/fs-subjects"

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of vittal korann 

Sent: Friday, February 24, 2023 11:56 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Failing to execute QDEC

External Email - Use Caution

Hi Freesurfer experts,

I am looking forward to resolve this issue.
Any help would be greatly appreciated!

With regards,
Vittal



On Wed, Feb 22, 2023 at 3:13 PM vittal korann 
mailto:vittalkor...@gmail.com>> wrote:
Hi Freesurfer experts,

I am trying to run Qdec on schizophrenia pre and post intervention scans.
I created .dat and .levels  files within the qdec folders and loaded the .dat 
file into qdec gui.
It is suddenly crashing when I select my design and hit the Analyze button.
And the same error message copied below from the terminal.

 Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh
--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu
 to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

Even though I renewed my license file, the issue still persists.
FYI I did use qdec in the past and am quite comfortable with it.
Also, I attached my license file if anything is missing.

Any help would be appreciated!

With regards
Vittal


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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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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] Freesurfer Digest, Vol 228, Issue 26

[Wighton, Paul]

Hi Juan,

It is possible, but not recommended because differing versions of FreeSurfer 
will introduce biases into the analysis.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Juan Rivas 

Sent: Thursday, February 23, 2023 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: juan carlos rivas nieto
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26

External Email - Use Caution

Hi, I have 2 samples with schizophrenic patients. The first one was analyzed 
with FreeSurfer version 6, and the second one with version 7. Is it possible to 
compare results using two different versions?
Juan Carlos Rivas, MD, PhD

El jue, 23 feb 2023 a las 9:16, 
mailto:freesurfer-requ...@nmr.mgh.harvard.edu>>
 escribió:
Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Visualizing transparent surface with non transparent
  annotations (Leonardo Tozzi)
   2. Failing to execute QDEC (vittal korann)
   3. Re: different clusters in mri_surfcluster output versus
  viewing in Freeview (Huang, Yujing)
   4. Re: segmenThalamicNuclei.sh exited with ERRORS (beh?et ayy?ld?z)
   5. Re: Extracting brain volume seperately (Douglas N. Greve)
   6. Re: Nuisance regressors (Douglas N. Greve)
   7. Please unsubscribe me (Manuela Dorado Novoa)
   8. Re: Hole in the insula (Douglas N. Greve)
   9. Re: Correlating and/or linear regressing surface overlays
  (Douglas N. Greve)
  10. Re: different clusters in mri_surfcluster output versus
  viewing in Freeview (Smith, Christine)
  11. Re: mri_easyreg tool (Iglesias Gonzalez, Juan E.)
  12.  MGH35 template (Maffei, Chiara,PHD)
  13. Re: [External] Re: 7.3.2-patch issues - thalamic segmentation
  (Kumar, Avnish)
  14. Re: mri_robust_register --minsize (Reuter, Martin,Ph.D.)
  15. Re: [External] Re: 7.3.2-patch issues - thalamic  segmentation
  (Aaron Tanenbaum)


--

Message: 1
Date: Wed, 22 Feb 2023 19:34:40 +
From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Subject: [Freesurfer] Visualizing transparent surface with non
transparent annotations
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:

mailto:byapr02mb5352e6f3cf76c8b3fc793bd0a9...@byapr02mb5352.namprd02.prod.outlook.com>>

Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Dear Experts,

I would like to use Freeview to achieve the following.

I would like to visualize a transparent brain surface, with only some 
annotations visible. In other words, I would like the surface to be 
transparent, but the annotations I choose to visualize to not be transparent.

Is there a way to achieve this?

Thank you,

Leonardo Tozzi, MD, PhD
Director of Computational Neuroscience & Neuroimaging Program
Stanford Center for Precision Mental Health and Wellness
Stanford University
lto...@stanford.edu>
 | (650) 5615738

Connect with us!
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Re: [Freesurfer] installation of two versions of freesurfer on same computer...

[Wighton, Paul]

Hi Gonzalo,

Download the .tar.gz files for the versions you're interested in and extract to 
different directories.
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/

Then to run a particular version, set the environment variable FREESURFER_HOME 
to the install directory of version you would like to use, then run

source $FREESURFER_HOME/SetUpFreeSurfer.sh

if using a bash terminal, or

source $FREESURFER_HOME/SetUpFreeSurfer.csh

if using a C shell terminal.

-Paul



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Gonzalo Rojas Costa 

Sent: Friday, February 3, 2023 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] installation of two versions of freesurfer on same
computer...

External Email - Use Caution

Hi:

  How can I install two different versions of freesurfer on the same computer?

  Sincerely,


Gonzalo Rojas Costa


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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] License issue

[Wighton, Paul]

Hi Chris,

What version of FreeSurfer are you using?  There are some issues with the 
license file with really old (<6.0) versions, but the 5.3-HCP version should 
work.

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sayre, Christopher 

Sent: Tuesday, January 31, 2023 12:21 PM
To: Freesurfer support list
Subject: [Freesurfer] License issue

External Email - Use Caution
Hello all,

I have gotten my license.txt file and I have copied it to the $FREESURFERHOME 
Directory. When attempting to use freesurfer I am getting the following error. 
Error parsing licensing file, expected 4 values. Looking at the file there are 
4 lines in the file.

Does anyone have any ideas?

Thanks,

Chris Sayre
Systems Engineer
Fralin Biomedical Research Institute at 
VTC
Health Sciences and Technology
2 Riverside Circle, Roanoke, VA 24016
O: 540-526-2012 | E: csa...@vtc.vt.edu
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] Regarding MRI Understanding.

[Wighton, Paul]

Andy's brain book and neurostars are other great resources

https://andysbrainbook.readthedocs.io/en/latest/index.html
https://neurostars.org/

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of FELICITY SIMPSON 

Sent: Tuesday, December 6, 2022 10:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Regarding MRI Understanding.


External Email - Use Caution

Hi all,

I am in a similar boat to Rahul and would like to teach myself more about 
neuroimaging, specifically, for my PhD I would like to determine a brain age 
gap (possibly using HCP/UKbiobank to train my model etc).
A colleague has recommended using datacamp to learn machine learning and coding 
in python. I was wondering whether there were any other resources that may be 
useful?

Kind regards,
Felicity


On Wed, Dec 7, 2022 at 7:33 AM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Rahul,

There is are a lot of resources on the "Teach Youself FreeSurfer" page
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Rahul Sharma 
mailto:sharmarahul.26...@gmail.com>>
Sent: Tuesday, December 6, 2022 1:02 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Regarding MRI Understanding.


External Email - Use Caution

Hello everyone, I am very new to this neuroimaging and belongs to technical 
background. Could anyone provide me any source or material for understanding 
MRI scans and the neuroimaging tools such as Freesurfer or FSL. Eagerly waiting 
for your reply.
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Re: [Freesurfer] Regarding MRI Understanding.

[Wighton, Paul]

Hi Rahul,

There is are a lot of resources on the "Teach Youself FreeSurfer" page
https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rahul Sharma 

Sent: Tuesday, December 6, 2022 1:02 PM
To: Freesurfer support list 
Subject: [Freesurfer] Regarding MRI Understanding.


External Email - Use Caution

Hello everyone, I am very new to this neuroimaging and belongs to technical 
background. Could anyone provide me any source or material for understanding 
MRI scans and the neuroimaging tools such as Freesurfer or FSL. Eagerly waiting 
for your reply.
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Re: [Freesurfer] FreeSurfer equivalent to fslsplit?

[Wighton, Paul]

Oh that's perfect, thanks Bruce!

-Paul

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

Sent: Tuesday, December 6, 2022 12:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer equivalent to fslsplit?


I think mri_convert can take a frame number. Something like:



mri_convert -nth 0 image.nii frame0.mgz

mri_convert -nth 1 image.nii frame1.mgz

.

.

.

Although that means you have to know how many frames are in the original file





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Tuesday, December 6, 2022 12:01 PM
To: Freesurfer support list 
Subject: [Freesurfer] FreeSurfer equivalent to fslsplit?



Hey FreeSurfer aficionados,



Is there a FreeSurfer equivalent to fslsplit?  If I have a 4d nifti, is there a 
way to split that into a set of 3d niftis from the command line?



Thanks,



-Paul
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continue to communicate over unencrypted e-mail. 

[Freesurfer] FreeSurfer equivalent to fslsplit?

[Wighton, Paul]

Hey FreeSurfer aficionados,

Is there a FreeSurfer equivalent to fslsplit?  If I have a 4d nifti, is there a 
way to split that into a set of 3d niftis from the command line?

Thanks,

-Paul
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] change in mask size

[Wighton, Paul]

Hi Padma,

You can use the --like flag of mri_convert to convert the output of the skull 
stripping back to the dimensions of the original file
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert

e.g

mri_convert  --like input-to-skullstrip.mgz output-from-skullstrip.mgz 
skullstripped_orig_dims.mgz

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Thursday, October 27, 2022 3:05 AM
To: Freesurfer support list 
Subject: [Freesurfer] change in mask size


External Email - Use Caution

Dear Team,

I tried using freesurfer for skull stripping and I got results all of size 
256X256X256 but the original data size is different, it's 512X512X537.

Is there any way to bring back the original size in freesurfer?
Any help would be appreciated.

Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/1X9_70aZZbsfnz1IFfS3bNa-LBmYH4f-7Rc-fpgIw_MEzjNJ9eRJo88rIbv3WBC4mYp5otUNZYdRpjs4o-D83gRQSMTsStLtiOd8IdlweeOOX7joye123osJtsPs6fg81LPr48sCkBxLbPkh8b4Qdjgv35mEAugsGwv99agSRzRQAa7brHnw1-K4Nbb-qAe9xz3fmUNSnVMAdtifnYlb5lnpd-mToYJhALvXVCZqGlSK5lBYBJv3xCfPWqAShutPOqTYyJB-koKTbI_wwy650qVtXxwMmVycpPwf3E3YiI0INkvJsAT7uBbMbaCeQDByJGRxhEHSh39HMD9bo0dmh3A/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai | (+82)10-5405-2685


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Re: [Freesurfer] conversion of .stats to .csv

[Wighton, Paul]

Hi Padma,

There is probably a 'cleaner' way to do this, but this should work:

cat aseg.stats |grep -v '#'|sed 's/ \{1,\}/,/g'|sed 's/^,//'|sed 's/,$//' > 
aseg.csv

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Wednesday, October 26, 2022 9:36 PM
To: Freesurfer support list 
Subject: [Freesurfer] conversion of .stats to .csv


External Email - Use Caution

Dear Team,

I would like to convert the .stats files that are being generated in the stats 
folder as an output from recon-all to csv file or excel file. Is there any way 
to convert .stats to .csv or .excel format? any help on this would be much 
appreciated.

Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/18su6ZmdWhUO0KseAqfEzoL3YRI-fCTh9PQy_6JGwGMgOqXSHX8kdUPJgrZrxDRlwiiDDpJ5m1wtmHphMELKMjvBwLSrN02yCt6GQHRKQ7hAGrIakc-YOGaZSD8TzBFC7PYQlRa7it6Kr0o-OsNcQ9tcYY_fxpvIrxuMsiqvC7q7twxfZZC6AWVn8j32Y1eIdqVVxpxFJoLRBOlXui7dD-F1g_ATGWoGGeFOTX8ucIo3P3AmFjlTI-Xy8mme20yXTdOKYHsJXXHeQH0vcUzg6i-mEJU4sx3OtUcxwvDSyBbaF09QR1fCDRR2xMwdkOpBapZ5T_P63AE46BsmI2EQ4kg/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai | (+82)10-5405-2685


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Re: [Freesurfer] mghread : cannot open the file

[Wighton, Paul]

Hi Padma,

The error is saying it can't find the file /mri/norm.mgz. Does that file exist? 
 What does `ls /mri/norm.mgz` return?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Wednesday, October 19, 2022 2:07 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mghread : cannot open the file


External Email - Use Caution

Hello Team,

Is there any solution for the above mentioned issue? I am still struck in the 
same place.

Thank you

On Fri, Oct 14, 2022 at 10:20 AM priya padma 
mailto:pr...@phenomx.ai>> wrote:
Hi Paul,

Thank you for your email. I tried how to told me

"mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129_ 
/mri/norm.mgz"

I gave this command, initially it used to give the error in the starting when 
it tries to load aseg,mgz file but now it shows error after few steps

~/Priya/freesurfer/subjects$ mri_compute_volume_fractions --o test --regheader 
sub-AD003S1059S61129_ /mri/norm.mgz
mri_compute_vol supposed to be reproducible but seed not set

7.3.2
sysname  Linux
hostname ai01
machine  x86_64
user phenomx
setenv SUBJECTS_DIR /home/phenomx/Priya/freesurfer/subjects
cd /home/phenomx/Priya/freesurfer/subjects
mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129_ 
/mri/norm.mgz
outstem test
regfile (null)
regtype 0
segfile aseg.mgz
wsurf white
psurf pial
TempVolFile /mri/norm.mgz
USF 2
Reading in aseg and surfs from 
/home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_
Loading 
/home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_/mri/aseg.mgz
Filling empty voxels with extracerebral CSF (if not there already), nDil=3
Loading orig 
/home/phenomx/Priya/freesurfer/subjects/sub-AD003S1059S61129_/mri/orig.mgz
Loading template /mri/norm.mgz
error: mghRead(/mri/norm.mgz, -1): could not open file

If I am not wrong, I believe the search is not directed to the right path, but 
when everything is right I donno how to solve this. Is there any solution ?

Thank you

On Fri, Oct 14, 2022 at 12:54 AM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Padma,

It can't find the file:
/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz

Are you trying to run this on a subject called sub-AD003S1059S61129?  If so, 
can you try:

mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129 
/mri/norm.mgz

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of priya padma mailto:pr...@phenomx.ai>>
Sent: Wednesday, October 12, 2022 10:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mghread : cannot open the file


External Email - Use Caution

Hello Team,

I am trying to find the volume of WM, GM, CSF separately and I came across this 
command namely
"mri_compute_volume_fractions"

Looking through all the email archives I gave the following line as the command 
after setting the paths

$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

but I get the following error


user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o 
test --regheader tester /mri/norm.mgz

 supposed to be reproducible but seed not set


7.3.2

sysname  Darwin

hostname user-MacBook-Pro.local

machine  x86_64

user 

setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects

cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129

mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

outstem test

regfile (null)

regtype 0

segfile aseg.mgz

wsurf white

psurf pial

TempVolFile /mri/norm.mgz

USF 2

Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/tester

Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz

error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, 
-1): could not open file



I set all the paths so why am I not able to read the mgz file?


Could anyone help me with this ?


Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/1Sii6Tv7lFwUl5uVc4ILyhApqN4giKhqzdQnct79ykzdW_zdK8r0ZQlm2mE0jHpXKjVEjwfvIdYdcRO8a5We0b5YvlNmi4Pv_Fd3i7osUc6MwxNI0kGVx-tLKJ8M85dkFqYvhpsTXEbLKDBH8rAQp3BiFF1a43XPnkuzgo8QcqXLwn2AEKShqltWugVEp6-9C32PnYZy0yNNe8R7iOEc4-zvCQY33659Er2xeYev8N0RvsEx4I7_cWEsccyX0XK-VtWgTjS2JtqUuVWHAQoFbVjakgJtb0bT_rgzlp0hg_nzDjNYWCDqc4QgwdHKhIl6ta77yuRKYnv3FRFCkPWTVFw/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai<mailto:pr...@phenomx.ai> | (+82)10-5405-2685


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Re: [Freesurfer] mghread : cannot open the file

[Wighton, Paul]

Hi Padma,

It can't find the file:
/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz

Are you trying to run this on a subject called sub-AD003S1059S61129?  If so, 
can you try:

mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129 
/mri/norm.mgz

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Wednesday, October 12, 2022 10:25 PM
To: Freesurfer support list 
Subject: [Freesurfer] mghread : cannot open the file


External Email - Use Caution

Hello Team,

I am trying to find the volume of WM, GM, CSF separately and I came across this 
command namely
"mri_compute_volume_fractions"

Looking through all the email archives I gave the following line as the command 
after setting the paths

$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

but I get the following error


user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions --o 
test --regheader tester /mri/norm.mgz

 supposed to be reproducible but seed not set


7.3.2

sysname  Darwin

hostname user-MacBook-Pro.local

machine  x86_64

user 

setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects

cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129

mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

outstem test

regfile (null)

regtype 0

segfile aseg.mgz

wsurf white

psurf pial

TempVolFile /mri/norm.mgz

USF 2

Reading in aseg and surfs from /Applications/freesurfer/7.3.2/subjects/tester

Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz

error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz, 
-1): could not open file



I set all the paths so why am I not able to read the mgz file?


Could anyone help me with this ?


Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/1Sii6Tv7lFwUl5uVc4ILyhApqN4giKhqzdQnct79ykzdW_zdK8r0ZQlm2mE0jHpXKjVEjwfvIdYdcRO8a5We0b5YvlNmi4Pv_Fd3i7osUc6MwxNI0kGVx-tLKJ8M85dkFqYvhpsTXEbLKDBH8rAQp3BiFF1a43XPnkuzgo8QcqXLwn2AEKShqltWugVEp6-9C32PnYZy0yNNe8R7iOEc4-zvCQY33659Er2xeYev8N0RvsEx4I7_cWEsccyX0XK-VtWgTjS2JtqUuVWHAQoFbVjakgJtb0bT_rgzlp0hg_nzDjNYWCDqc4QgwdHKhIl6ta77yuRKYnv3FRFCkPWTVFw/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai | (+82)10-5405-2685


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Re: [Freesurfer] Running recon-all in parallel

[Wighton, Paul]

Hi Padma,

It looks like tcsh isn't installed.  Can you try installing it by running

```
sudo apt update
sudo apt install tcsh
```

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Wednesday, October 12, 2022 3:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Running recon-all in parallel


External Email - Use Caution

Hello team,

As freesurfer takes lot of time for processing one subject, I was searching on 
how to run recon-all for multiple subjects in parallel and I found the 
following in Andy's brain book doc

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_04_ReconAllParallel.html

and ran

$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache

and I get the error "/usr/bin/bash: /home/***/***/freesurfer/bin/recon-all: 
/bin/tcsh: bad interpreter: No such file or directory "

I believe that this is not the right command for linux, ubuntu 20 OS but I am 
not sure.

Could anyone help me with this?

Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/1XLVnI0aLlqbfbCotrXgyfGAqS76ynzDA16AK0UPYPBFVyMmcGdjYw13PRbu_GL-p855BsKJU9SklwJQSakQKpxHv5eMf2-laEUBjeva9dcHFAZapnnIf93hWg8pRAWbVcg-2MydVNiXmXBj-YmWq-bH0WE41eoRC00Ckz8H1it778wY8pz28_aRWuDtNfpUn8HQutOjBgPcWHG3LdEfx0Kd7gMeX1I6sOkQq-0Z8G_WOM8MvElrz2q3TpU2zG9XFRelH-mh5Reodau1XKrdoVh54-bfua-fWehURa_uA1CwdSxNM_-9MyX9uYRF1sRe6-R7mEFWx1h4ogvwU4F4RuQ/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai | (+82)10-5405-2685


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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 
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 .
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Re: [Freesurfer] Error while testing FS version 5.1

[Wighton, Paul]

Hi Leema,

This is a known issue.  It has to do with the behaviour of the crypt() function 
provided by glibc, which has changed in more recent versions of ubuntu.  We 
don't have a solution for it at this time, unfortunately.

If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism 
should work, or you could upgrade your version of FreeSurfer.  If neither of 
those options are possible, you could run FreeSurfer inside a docker or 
singularity container derived from ubuntu 16.04.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of leema_mur...@eisai.com 

Sent: Wednesday, October 5, 2022 8:43 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FW: Error while testing FS version 5.1


External Email - Use Caution

Hello FreeSurfer Developers,



I’m trying to use Freesurfer version 5.1 for my work. I get errors based on 
invalid license even though I have provided the right license within 
$FREESURFER_HOME/.license



Is there a specific way to define the license file for 5.1 version. I have been 
using the latest version before and I had just added the license.txt with 
$FREESURFER_HOME.



Please can anyone help me to troubleshoot this  issue.



Platform: Ubuntu 18.04

Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

recon-all.log: see attached



[cid:image001.png@01D8D895.A24160F0]



Looking forward for you reply.



Thank you,

Leema


[This e-mail message may contain privileged, confidential and/or proprietary 
information of Eisai. If you believe that it has been sent to you in error, 
please contact the sender immediately and delete the message including any 
attachments, without copying, using, or distributing any of the information 
contained therein. This e-mail message should not be interpreted to include a 
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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 
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 .
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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] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Since this is the VM, one thing to try is to follow along with the instructions 
here
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify

Particularly the part where 3d acceleration is disabled.  If that doesn't work, 
please start a new thread.

Good luck!

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Friday, September 30, 2022 10:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

hi Paul,

yes that’s right, i can ask again in the freesurfer mailing list if someone 
else can help with this. I’m trying to run Freeview inside the Freesurfer 
virtual machine using Ubuntu 20 on the linux windows operating system. It seems 
to be running again but doesn’t show me any images
Thanks for the help!

Sincerely,
Justina

On Fri, Sep 30, 2022 at 4:18 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

I don't know too much about FreeView, unfortunately.  Hopefully others on the 
list have some ideas.

Are you trying to run FreeView inside the FreeSurfer virtual machine?  What 
operating system are you using?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Friday, September 30, 2022 5:36 AM

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come across 
the issue with loading data and seeing nothing on freeview. Hope you can help 
me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee 
mailto:justinale...@gmail.com>> wrote:
Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable to 
solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open any 
data, I seem to not see anything. Upon trying again recently, now opening 
freeview does not seem to work at all. (For example, trying to run the command 
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally loc

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

I don't know too much about FreeView, unfortunately.  Hopefully others on the 
list have some ideas.

Are you trying to run FreeView inside the FreeSurfer virtual machine?  What 
operating system are you using?

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Friday, September 30, 2022 5:36 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come across 
the issue with loading data and seeing nothing on freeview. Hope you can help 
me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee 
mailto:justinale...@gmail.com>> wrote:
Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable to 
solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open any 
data, I seem to not see anything. Upon trying again recently, now opening 
freeview does not seem to work at all. (For example, trying to run the command 
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=0

Re: [Freesurfer] Voxel to mm coordinates

[Wighton, Paul]

Hi Panos,

Yes that is correct.  Taking a voxel value and multiplying it by the vox2ras 
matrix will give you a coordinate in the "patient coordinate system" which is 
in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are 
positive.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fotiadis, Panagiotis 

Sent: Wednesday, September 21, 2022 5:07 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Voxel to mm coordinates


External Email - Use Caution

Hello,



I was wondering what the best way would be to extract the coordinates of each 
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume 
into Matlab (=mri) and wanted to essentially create a new variable that takes 
each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I 
just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ 
(where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different 
steps involved?



Thank you in advance for your time and help!



Best,

Panos
___
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] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

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

Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0<http://secure-web.cisco.com/1-hejosJTLRC2vV-OfdCSe_uY8hHvMUDjci5bJsNGZn55Ex_VuIMtvmOuJdpL7qWdzXWDGWXTu8KGwGjHhDnfNs_Oz9looUNIOEBEBDEhKbiE_unv86fZj2sikQ0C0-tHyqn_l6wkDU_YWnG6DV3QHzjtYNloKKHEuKAgZ0pB0BV4tlM4606CV71h7g44f_CnbhyUAiGY6ITBFhskq654vl-8YehA-4iHy8efSL8oarabfltq8DZl-xQhNFFPsqGFEXKF7G2k0L2szdfOQvb6GN2jH9O1S832tDcli4qEUuOwNLR1x02kQiybtiDrvGm-/http%3A%2F%2F172.25.144.1%3A0>
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfe

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program
 
Files/MATLAB/R2022a/bin:/mnt/c/Users/lenovo/AppData/Local/Microsoft/WindowsApps:/snap/bin
FSF_OUTPUT_FORMAT=nii.gz
HOSTTYPE=x86_64
PULSE_SERVER=/mnt/wslg/PulseServer
_=/usr/bin/env
OLDPWD=/home/ylee6/ADIPA_data

Finally, I am running the segmentHA_T1.sh command under this pathway:

ylee6@LAPTOP-63HA9ANS:~/ADIPA_data/26/mri$ segmentHA_T1.sh 26

resulting in the error that I have shown previously but described again below:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I believe that you are right that the SUBJECTS_DIR environment isn't set 
correctly, so I followed the subjects directory stated in the 'env' command and 
tried the command again as such:

ylee6@LAPTOP-63HA9ANS:~/ADIPA_data/26/mri$ segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]

Hence resulting in the following commands:

getfullpath: No match.
if: Missing file name.

Could it be that the data from the recon-all for the subject is not in the 
subject directory but in the other file (ADIPA_data), hence unable to run the 
command? When I open the folder for subject 00026 on windows, I only find one 
file in it, which is ' EchoCombination_f02g01_bet.nii.' In this folder under 
the subject directory stated above (/usr/local/freesurfer/7.3.2/subjects), it 
does not have the find 'wmparc.mgz,' 'norm.mgz,' or 'talairach.xfm' it needs.

If the problem lies that the files are not in the corresponding folders, could 
you be able to tell me (as you already know I am a new learning student of 
linux system) how I can move these files instead of through my computer 
manually? Does the problem lie somewhere else?

Thank you and I appreciate your time and efforts.

Sincerely,
Justina


On Wed, Sep 14, 2022 at 5:07 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Can you send the following:
  - The recon-all.log file for the subject you are trying to run through 
segmentHA_T1.sh
  - The output from running the `env` command
  - The command you are using to invoke segmentHA_T1.sh

My guess is that the SUBJECTS_DIR environment variable isn't set correctly, but 
we should also double check that recon-all completed successfully.

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Wednesday, September 14, 2022 3:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

This seems to have done the trick. Thank you for guiding me through this 
process, I really appreciate all your help.

My last question refers to this comment when trying to run the segmentHA_T1.sh 
command:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I am sure that I am referring to the right path where the files are located as 
well as processing the subject with recon-all already. Is there something that 
I am missing?

Thank you so much for your time.

Sincerely,
Justina


On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
I think we are on the right track, but it looks like there was a space between 
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space 
between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME 
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME 

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Can you send the following:
  - The recon-all.log file for the subject you are trying to run through 
segmentHA_T1.sh
  - The output from running the `env` command
  - The command you are using to invoke segmentHA_T1.sh

My guess is that the SUBJECTS_DIR environment variable isn't set correctly, but 
we should also double check that recon-all completed successfully.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Wednesday, September 14, 2022 3:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

This seems to have done the trick. Thank you for guiding me through this 
process, I really appreciate all your help.

My last question refers to this comment when trying to run the segmentHA_T1.sh 
command:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I am sure that I am referring to the right path where the files are located as 
well as processing the subject with recon-all already. Is there something that 
I am missing?

Thank you so much for your time.

Sincerely,
Justina


On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
I think we are on the right track, but it looks like there was a space between 
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space 
between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME 
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

I think we are on the right track, but it looks like there was a space between 
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space 
between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME 
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

Fr

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of You Na Lee mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Spee

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

[Wighton, Paul]

Thanks R, those are very good points.

-Paul

From: fsbuild 
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: r.lud...@eni-g.de ; Wighton, Paul 
; fsbu...@contbay.com 
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu


External Email - Use Caution

The glibc version has changed in newer versions of Ubuntu.  That and/or changes 
to encryption related functions is likely preventing the license decoding from 
working.   Binary backwards compatibility cannot assure old binaries will 
indefinitely run on newer releases of the operating system., e.g., CentOS6 
binaries may not run on CentOS8.  Freesurfer 5.3 was released in 2013 at the 
time of Ubuntu 12 so I would not assume it will run on Ubuntu 18 and/or newer 
versions.  I don['t think LD_LIBRARY_PATH will help with statically linked 
binaries - and sertting it to point to a version could break dynamically linked 
binaries with RPATH strings.  In general it is a bad idea to be running with 
different versions of glibc on the same system.

There is an Ubuntu 12 VM running Freesurfer 5.3 available from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz<https://secure-web.cisco.com/13_Z5mhms1Dpq_WEjE79lEciW_21298e4jPP1NTDsZfB8Igfsnnu3qYl3BeyM76R9HGTX5lxisLN47qGSSeHCN3PAWPWaLY0swK-cyJZamxaMUeok9Y0urSrvDuG7EXCubWSA3M94NvLmMuwxWo8LWS7hCY67NvQdwSYhtCSqCRyqvpp1Goknf5X8rRc0NCmHs7-L7zGrDXU1W5kOLf63Mk6ffRDL39v9CdhvyvDG9umhsQ0VhOFfdRF6EeAKHLTgPTCv-FmbijBEd2vF73cPSHsNyOyqNt9aB4ywSLhNzB1ro12Z78khyvHF8cXPQ3rz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz>
   That VM still runs in VirtualBox on todays operating systems.

- R.

On Sep 13, 2022, at 13:28, Wighton, Paul  wrote:

Hi Rüdiger,

This is really interesting..  I'm able to reproduce this issue in a docker 
container.  Anyone else who would like to reproduce or look into this issue can 
use the following containers

- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 
(glibc v2.23) and everything works as expected in this container.
- The container `pwighton/freesurfer:5..3.0-HCP-focal` is based off of ubuntu 
20.04 (glib2 v2.31) and I am experiencing the same issue you describe.
- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 
and has the latest version of FreeSurfer installed.  Everything works as 
expected in this container.

So the issue seems to be some interaction between the v5.3 license checking 
code and the crypt() function provided by different versions of glibc, but that 
is just speculation at this point.

I'm sorry I don't have any solution for this at the moment.  You mention you 
are using lmod, would it be possible to define LD_LIBRARY_PATH inside the 
FreeSurfer 5.3 module to point to an older version of glibc?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ludwig, Rüdiger 

Sent: Tuesday, September 13, 2022 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again,

I realized I might have missed some important information in my question about 
freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  
for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper 
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a 
brand new license file, and one that still works for freesurfer 5.3 on our 
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or 
freesurfer 7.3

If you need any further information to help us, we am more than willing to 
provide that.

Thank you so much in advance

Ruediger

---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max 
Planck Society
Grisebachstr. 5
37077 Göttingen

Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051

___
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 p

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of You Na Lee mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Speed

100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not 
found



I am currently struggling to find the solution to this issue. Is the 
installation not in the correct path? Is MATLAB Runtime installed at all? 
Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







Sent from 
Mail<https://secure-web.cisco.com/1JF-rDYMVgKJTrVPsWHUacVbsZGxWoxGE8qofNJGanBLzB5H4xG_TSIyr-kKCyfB-OL5ahOLtropBWGT0WNStX9nlY96XmLI4PEcLyxRbpYACqwCkjWGnJ97rPRssexnOq1RJRlrOg_69B_HLSu5yX5bgMIHOh0IfF9pQcTT3TVu3DK8hZxWZSK0gfICgCNrQacXt91cfezI3FeQnjTGxoKqOqzHBsXJaNuI8JxuVMfCrweNj79o9pN5_cVgjrPSCSa5uR_IxkKANQ87K9laDUXpbpf1YpKyxu3k05hdqJLTPSgkt-wfEOgojaS7t3BsJWoxyJ2fHAPhk2SP958H0aA/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>
 for Windows



___
Freesurfer m

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

[Wighton, Paul]

Hi Rüdiger,

This is really interesting..  I'm able to reproduce this issue in a docker 
container.  Anyone else who would like to reproduce or look into this issue can 
use the following containers

- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 
(glibc v2.23) and everything works as expected in this container.
- The container `pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 
20.04 (glib2 v2.31) and I am experiencing the same issue you describe.
- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 
and has the latest version of FreeSurfer installed.  Everything works as 
expected in this container.

So the issue seems to be some interaction between the v5.3 license checking 
code and the crypt() function provided by different versions of glibc, but that 
is just speculation at this point.

I'm sorry I don't have any solution for this at the moment.  You mention you 
are using lmod, would it be possible to define LD_LIBRARY_PATH inside the 
FreeSurfer 5.3 module to point to an older version of glibc?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ludwig, Rüdiger 

Sent: Tuesday, September 13, 2022 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again,

I realized I might have missed some important information in my question about 
freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  
for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper 
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a 
brand new license file, and one that still works for freesurfer 5.3 on our 
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or 
freesurfer 7.3

If you need any further information to help us, we am more than willing to 
provide that.

Thank you so much in advance

Ruediger

---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max 
Planck Society
Grisebachstr. 5
37077 Göttingen

Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051

___
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] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

It looks like the matlab installer is trying to use unzip​ but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of You Na Lee 

Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Speed

100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not 
found



I am currently struggling to find the solution to this issue. Is the 
installation not in the correct path? Is MATLAB Runtime installed at all? 
Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







Sent from 
Mail
 for Windows


___
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] Docker for Freesurfer 7.3.2

[Wighton, Paul]

I just made a PR to neurodocker to support FreeSufer 7.3.2
https://github.com/ReproNim/neurodocker/pull/469

And used that to build the container `pwighton/freesurfer:7.3.2`.  I'm pushing 
it to dockerhub now.  It should be available in an hour or so.  It hasn't been 
tested yet, so if folks use it let us know how it goes!

You'll have to mount your FreeSurfer license file and tell FreeSurfer where 
it's located, e.g.
```
docker run -it --rm \
  -v ~/Downloads/license.txt:/license.txt:ro \
  -e FS_LICENSE='/license.txt' \
  ...
  pwighton/freesurfer:7.3.2 \
...
```

For reference, the container `pwighton/freesurfer:7.3.2` was built using the 
following command:
```
docker run pwighton/neurodocker:20220822 generate docker \
  --base-image ubuntu:xenial \
  --pkg-manager apt \
  --yes \
  --freesurfer \
method=binaries \
version=7.3.2 \
| docker build --no-cache --network host -t pwighton/freesurfer:7.3.2 - 
```

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Saturday, August 20, 2022 9:31 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: william.h.r...@vanderbilt.edu 
Subject: Re: [Freesurfer] Docker for Freesurfer 7.3.2


External Email - Use Caution

Hello Hudson,

It should work with an existing CentOS 7, 8 or Ubuntu 18, 20, 22 OS image that 
you already have running in docker to download and install the freesurfer 7.3.2 
.rpm or .deb package.  You just need to download the Freesurfer 7.3.2 package 
that matches your OS into the container from 
https://freesurfer.net/fswiki/rel7downloads and install it locally, e.g.,

… inside your container use wget or curl from the command line to fetch the 
package ...
$ cd /tmp
$ wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/
… for rpm file (RedHat, CentOS) ...
$ sudo yum install ./
… for deb file (Ubuntu) …
$ sudo apt-get install ./
… answer yes to queries if you want to commit to installing what will be added 
to the system …

When the installation finishes, look to see you have a subdirectory under 
/usr/local/freesurfer named after the 7.3.2 release, e.g., something like 
/usr/local/freesurfer/7.3.2.  That path should become the setting for the 
environment variable FREESURFER_HOME.

- R.

On Aug 20, 2022, at 17:05, Robb, William Hudson  
wrote:

External Email - Use Caution


Hello,

When is the Freesurfer 7.3.2 docker expected to be released? I see 7.2.0 
available here but not 7.3.2 : MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://hub.docker.com/r/freesurfer/freesurfer/tags

Thank you,
Hudson Robb
___
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The information in this e-mail is intended only for the person to whom it is 
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 .
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 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Problem with sxconcat-sess

[Wighton, Paul]

Thanks Noah,

This looks like an output.  Are you able to re-run the first level PCC_BOLD 
analysis and look for errors?

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Friday, July 1, 2022 2:40 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Paul,

The PCC_BOLD is just a directory name used for the analysis.

Please find the dof attached.

Thanks for your help.

Best wishes,
Noah

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

Sent: 30 June 2022 17:36
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Noah,

These dof files were not created by recon-all.  I was hoping there would be 
other log files in the scripts directory describing the functional analysis.

I have no idea what these dof files are, but they look to be either inputs to 
or outputs from a first-level BOLD analysis.  Does the term 'PCC_Bold' mean 
anything to you?

Can you share one of these dof files so we can see what they look like?

-Paul



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Wednesday, June 29, 2022 4:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Paul,

Thanks for your suggestion.

I examined all files within the /script directory from recon-all from two 
subjects where one subject created a dof, and another did not generate a dof. I 
used the vimdiff command to explore differences in the files. There were 
significant differences in three of the log files (from each subject); please 
be aware that I am new to FreeSurfer, and I am not sure what these differences 
indicate. For your convenience, I attached the files (.zip) and deidentified 
subject-specific information with "Subject_with_dof" or "Subject_with_no_dof".

What can I do to create the dof files to carry on with my analyses? Any 
suggestions are very much appreciated.

Thank you in advance for your help.

Best wishes,
Noah

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

Sent: 28 June 2022 11:10
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Noah,

I'm not super familiar with the functional stream, but it looks like something 
has gone wrong during the first-level analysis for some of your subjects.

Can you compare the log files in the ./scripts directory for a subject that has 
the dof files vs a subject that doesn't and post any differences you find?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Tuesday, June 28, 2022 8:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Problem with sxconcat-sess

Hello,

I am trying to concatenate my functional data with the following command (Ps: I 
am relatively new to FreeSurfer):

sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R 
-contrast bilateral_isthmuscingulate_bold_config -o DMN_Right.

I get an error that says the dof file cannot be found for my 26 scans in 
$SUBJECTS_DIR. However, running:

find . -name "dof"

The dof file was created for 12 scans. I used the same analysis pipeline for 
all the scans. I searched the mailing list, and haven't found anything that 
could help my problem. Any idea why the dof was not created for all scans? How 
can I create the dof for the remaining scans? Please let me know if you need 
further details. I am using Freesurfer version 6.0.0.

Any help is very much appreciated.

Please find the terminal output below.

Best wishes,
Noah



actrumri[0]:RECONS$ echo $SUBJECTS_DIR
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Right
DMN_Right/PCC_Bold_R/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_02

Re: [Freesurfer] Problem with sxconcat-sess

[Wighton, Paul]

Hi Noah,

These dof files were not created by recon-all.  I was hoping there would be 
other log files in the scripts directory describing the functional analysis.

I have no idea what these dof files are, but they look to be either inputs to 
or outputs from a first-level BOLD analysis.  Does the term 'PCC_Bold' mean 
anything to you?

Can you share one of these dof files so we can see what they look like?

-Paul



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Wednesday, June 29, 2022 4:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Paul,

Thanks for your suggestion.

I examined all files within the /script directory from recon-all from two 
subjects where one subject created a dof, and another did not generate a dof. I 
used the vimdiff command to explore differences in the files. There were 
significant differences in three of the log files (from each subject); please 
be aware that I am new to FreeSurfer, and I am not sure what these differences 
indicate. For your convenience, I attached the files (.zip) and deidentified 
subject-specific information with "Subject_with_dof" or "Subject_with_no_dof".

What can I do to create the dof files to carry on with my analyses? Any 
suggestions are very much appreciated.

Thank you in advance for your help.

Best wishes,
Noah

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

Sent: 28 June 2022 11:10
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with sxconcat-sess

Hi Noah,

I'm not super familiar with the functional stream, but it looks like something 
has gone wrong during the first-level analysis for some of your subjects.

Can you compare the log files in the ./scripts directory for a subject that has 
the dof files vs a subject that doesn't and post any differences you find?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Tuesday, June 28, 2022 8:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Problem with sxconcat-sess

Hello,

I am trying to concatenate my functional data with the following command (Ps: I 
am relatively new to FreeSurfer):

sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R 
-contrast bilateral_isthmuscingulate_bold_config -o DMN_Right.

I get an error that says the dof file cannot be found for my 26 scans in 
$SUBJECTS_DIR. However, running:

find . -name "dof"

The dof file was created for 12 scans. I used the same analysis pipeline for 
all the scans. I searched the mailing list, and haven't found anything that 
could help my problem. Any idea why the dof was not created for all scans? How 
can I create the dof for the remaining scans? Please let me know if you need 
further details. I am using Freesurfer version 6.0.0.

Any help is very much appreciated.

Please find the terminal output below.

Best wishes,
Noah



actrumri[0]:RECONS$ echo $SUBJECTS_DIR
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Right
DMN_Right/PCC_Bold_R/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Left
DMN_Left/PCC_Bold_L/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_66

Re: [Freesurfer] Command Not Found

[Wighton, Paul]

Hi Rachel,

Are you trying to run tkregister2?  Looks like you forgot the t at the start of 
the command.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Wagner 

Sent: Tuesday, June 28, 2022 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Command Not Found


External Email - Use Caution

Hello,



Thank you for your help! I am trying to register my spm image and am getting 
the following error:



developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz 
--regheader --reg register.dat --surf orig

kregister2: command not found





Is my path not set correctly?



Thanks again,

Rachel Wagner
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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 
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 .
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] Problem with sxconcat-sess

[Wighton, Paul]

Hi Noah,

I'm not super familiar with the functional stream, but it looks like something 
has gone wrong during the first-level analysis for some of your subjects.

Can you compare the log files in the ./scripts directory for a subject that has 
the dof files vs a subject that doesn't and post any differences you find?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shapiro, Noah Lorenz 

Sent: Tuesday, June 28, 2022 8:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Problem with sxconcat-sess

Hello,

I am trying to concatenate my functional data with the following command (Ps: I 
am relatively new to FreeSurfer):

sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R 
-contrast bilateral_isthmuscingulate_bold_config -o DMN_Right.

I get an error that says the dof file cannot be found for my 26 scans in 
$SUBJECTS_DIR. However, running:

find . -name "dof"

The dof file was created for 12 scans. I used the same analysis pipeline for 
all the scans. I searched the mailing list, and haven't found anything that 
could help my problem. Any idea why the dof was not created for all scans? How 
can I create the dof for the remaining scans? Please let me know if you need 
further details. I am using Freesurfer version 6.0.0.

Any help is very much appreciated.

Please find the terminal output below.

Best wishes,
Noah



actrumri[0]:RECONS$ echo $SUBJECTS_DIR
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Right
DMN_Right/PCC_Bold_R/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects 
-analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o 
DMN_Left
DMN_Left/PCC_Bold_L/log/isxconcat.log
ERROR: cannot find 
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$
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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] aseg.stats - eTIV volume space

[Wighton, Paul]

Hi Katie,

FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of 
1mm^3 and sagittal orientation.

You can compare orig.mgz to the original input to see what the difference 
between native space and FreeSurfer Space would be.

eTIV is computed using the transformation matrix from FreeSurfer Space to 
MNI305 space.  There is more information here about it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Thursday, June 23, 2022 6:08 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] aseg.stats - eTIV volume space


External Email - Use Caution

Hi FreeSurfer experts,

I apologize if this question has been addressed, but I was unable to find a 
definitive answer elsewhere.

I am using the aseg.stats file to extract the estimated Total Intracranial 
Volume (eTIV) value to be used as a correction to my anatomical data. I just 
want to confirm what space this data is in. I had previously assumed this data 
was in native anatomical space. But I read on the wiki that this statistic is 
calculated using the Talairach transform file (talairach.xfm), which is the 
conversion from MNI305 to Talairach. I just want to ensure I am correct in the 
assumption that this data is represented in native anatomical space.

Thank you so much for your help in this matter.

Best Wishes,
Katie

--
Katie Jobson, M.S.
PhD Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University
[cid:dcfe96a7-bf68-4d92-8c1e-61f5814893fa]
___
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] TRACULA -bedp parallel processing

[Wighton, Paul]

Hi Ela,

It looks to me like line 79 of bedpostx_preproc.sh is:

if [ ${gflag} -eq 1 ]; then

Which is consistent with the error:

-eq: unary operator expected

What this error is saying is that the variable `gflag` has not been set, so the 
script does not know how to perform the comparison.

`gflag` is set a few lines above to the second parameter passed when executing 
`bedpostx_preproc.sh`.  I would investigate how `bedpostx_preproc.sh` is being 
invoked to chase down the cause of this error.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

That actually helps but not solving all the problems. So, what happens is that 
if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target 
'/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a 
directory). However, the second error still exists: a.k.a. 
(home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And 
when I try to run Parallel lines, I still get the error 
(dmri.bedpostX/logs/log: No such file or directory). So, my guess is, it 
still doesn't copy the whole needed package for some reason. So, what we end up 
having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.

I can always manually copy all needed file from fsl folder to our subjects 
folder, but I am curious why we get the error and why everything is not copied 
automatically. I also don't know what files we need to manually copy.

Thanks again,
Ela

From: Yendiki, Anastasia 
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What if you create the directory (that shows up in the "not a directory" error)?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
Anastasia

Sent: Mon, 06 Jun 2022 20:17:47 

Re: [Freesurfer] vertex ID in the contralateral hemisphere

[Wighton, Paul]

Hi Marina,

I believe mris_left_right_register can do this.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Marina Fern?ndez 

Sent: Tuesday, June 7, 2022 4:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] vertex ID in the contralateral hemisphere


External Email - Use Caution

Dear experts,

I would like to know the corresponding vertex in the contralateral hemisphere 
of a given vertex. Do you have a function that allows me to know it?

Thank you very much in advance.

Best regards,
Marina
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Re: [Freesurfer] Starting a new project

[Wighton, Paul]

Hi Raffaele,

There is some info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide

For more details on compiling FreeSurfer from source, you can refer to this 
neurodocker template:
https://github.com/ReproNim/neurodocker/blob/12d0f21e119ad595ccf2487b4edc788a6e032dc3/neurodocker/templates/freesurfer.yaml#L260

Which documents exact versions of gcc, cmake, python etc. and is part of this 
pull request:
https://github.com/ReproNim/neurodocker/pull/445

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Raffaele Di Natale 

Sent: Wednesday, May 25, 2022 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Starting a new project


External Email - Use Caution

Hello FreeSurfer Developers,


I'm attempting to develop new functions in the tool for my research activity 
and I wish to know if there is a guide about to start this kind of activity.


1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz


Raffaele Di Natale, PhD
Contract Researcher
DIEEI, University of Catania
+39 095738 2385 (Edificio 13)
+39 095738 7903 
(OpenLab)
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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] Deface DICOM

[Wighton, Paul]

Hi Victor,

If you have the original DICOMs you could try something like pydicom to 
overwrite the voxel values.  The process would go something like:

1) Convert DICOM to nifti using your favorite tool
2) Deface niftii data using your favorite tool
3) Load the defaced data into python using nibabel,
4) Load the original dicom data into python using pydicom
5) Overwrite voxel values in the dicom with defaced nifti data
6) Use pydicom to save a new defaced DICOM series

Good luck!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Victor Montal Blancafort 

Sent: Tuesday, May 24, 2022 10:39 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Deface DICOM


External Email - Use Caution

Dear FS experts,

I am using mri_deface to annon our data. Nevertheless, for a recent project, we 
were requested to share our DICOM original files, instad of .nii or .mgz.
Thus, I was wondering if you know a simple way to deface T1 data inputing a 
DICOM and obtaining a series of DICOM as output?

I have tried to
   1) deface using mri_deface,
   2) convert the .nii to dicom using the nifti2dicom utility and
   3) correct DICOM info thats incorrecly parsed at step 2).

However,  such approach does not work correctly for all our data (it fails for 
several reasons, such as correctly storing acq direction, or dimensions when 
sampling from nifti 2 dicom).

I have seen that @Doug has been working on a new deface utility (mideface) but 
it seems to work also only for .nii

Any insight?
Victor Montal
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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: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Wighton, Paul]

Hmm, ok that's not the issue.  You have plenty of free disk space (185Gb)

Is the folder /home/developer/guest_shared shared with the host OS (windows)? 
That could be the issue as windows does not support symbolic links.  Could you 
try changing the subject's directory to something that is not shared with the 
host OS?

e.g:
```
mkdir -p /home/developer/fs-subjects
export SUBJECTS_DIR=/home/developer/fs-subjects
```

And then try running recon-all again?

My apologies.  This is my fault as I originally suggested that location for the 
subjects directory. Also, thanks to R. for his help diagnosing this issue!

-Paul

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

Sent: Friday, May 6, 2022 2:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


External Email - Use Caution

Hi Paul,

I have everything on my Data (D:) drive because my OS (C:) drive was already 
nearly full when I began this process of downloading FreeSurfer and knew it 
wouldn't have enough space. Is that a problem that I am using the D: drive? (I 
am not too familiar with the differences between the two).

Pasted below is the output of df --si.

Thank you for your help!
Joanna

developer@developer-VirtualBox:~/guest_shared/fs-subjects$ df --si
Filesystem  Size  Used Avail Use% Mounted on
udev4.2G 0  4.2G   0% /dev
tmpfs   835M  1.6M  833M   1% /run
/dev/sda1   216G   21G  185G  10% /
tmpfs   4.2G 0  4.2G   0% /dev/shm
tmpfs   5.3M  4.1k  5.3M   1% /run/lock
tmpfs   4.2G 0  4.2G   0% /sys/fs/cgroup
/dev/loop0   69M   69M 0 100% /snap/gtk-common-themes/1519
/dev/loop1  230M  230M 0 100% /snap/gnome-3-34-1804/72
/dev/loop3   47M   47M 0 100% /snap/snapd/15534
/dev/loop2   46M   46M 0 100% /snap/snapd/15177
/dev/loop6  787k  787k 0 100% /snap/gnome-characters/726
/dev/loop5  2.8M  2.8M 0 100% /snap/gnome-calculator/920
/dev/loop4  787k  787k 0 100% /snap/gnome-characters/741
/dev/loop7  230M  230M 0 100% /snap/gnome-3-34-1804/77
/dev/loop9  254M  254M 0 100% /snap/gnome-3-38-2004/70
/dev/loop8  2.8M  2.8M 0 100% /snap/gnome-system-monitor/174
/dev/loop10  66M   66M 0 100% /snap/core20/1434
/dev/loop11 132k  132k 0 100% /snap/bare/5
/dev/loop12  69M   69M 0 100% /snap/gtk-common-themes/1515
/dev/loop13 656k  656k 0 100% /snap/gnome-logs/106
/dev/loop15  59M   59M 0 100% /snap/core18/2128
/dev/loop14 2.7M  2.7M 0 100% /snap/gnome-system-monitor/163
/dev/loop16 261M  261M 0 100% /snap/gnome-3-38-2004/99
/dev/loop17  59M   59M 0 100% /snap/core18/2344
/dev/loop18 2.7M  2.7M 0 100% /snap/gnome-calculator/884
/dev/loop19  66M   66M 0 100% /snap/core20/1376
tmpfs   835M   17k  835M   1% /run/user/121
tmpfs   835M   46k  835M   1% /run/user/1000
shared  1.1T   48G  953G   5% /home/developer/guest_shared




--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


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

Sent: Friday, May 6, 2022 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"

Hi Joanna,

Is it possible you've run out of disk space?  What's the output of `df --si`?

-Paul

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

Sent: Friday, May 6, 2022 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


External Email - Use Caution

Dear FreeSurfer Team,

I am attempting to run Recon-all on practice cannabis data on the tutorial, 
using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu).

On my first attempt to run Recon-all, I got the error shown below: "ln: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux 

Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Wighton, Paul]

Hi Joanna,

Is it possible you've run out of disk space?  What's the output of `df --si`?

-Paul

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

Sent: Friday, May 6, 2022 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


External Email - Use Caution

Dear FreeSurfer Team,

I am attempting to run Recon-all on practice cannabis data on the tutorial, 
using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu).

On my first attempt to run Recon-all, I got the error shown below: "ln: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
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-sesBL exited with ERRORS at Thu May  5 23:34:17 EDT 2022

For more details, see the log file 
/home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




After searching through the archives, I see that other people have had the same 
problem in that their os is not able to create a symbolic link.  I tried 
following one of the archives and did:



developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$
 cd /home/developer/guest_shared/fs-subjects
developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s 
/home/developer/guest_shared/fs-subjects/fsaverage
ln: failed to create symbolic link './fsaverage': Operation not permitted

But I again received the "failed to create symbolic link. How can I allow 
symbolic links? Also, I was generally wondering how do you rerun recon-all 
starting from a specific step once I get this working? Does one have to rerun 
all of recon-all each time there is an error or can I start from where I left 
off?

Thank you so much for your help!

Best wishes,
Joanna

___
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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"

[Wighton, Paul]

Thanks Joanna, that's great to hear!

-Paul

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

Sent: Thursday, May 5, 2022 8:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"


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 MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfe

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

[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

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Re: [Freesurfer] Scalable recon workflow

[Wighton, Paul]

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 
mailto:mjh...@mgh.harvard.edu>> 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









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