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Today's Topics:

   1. Re: Fail to install FreeSurfer 7 from the *.deb package (fsbuild)
   2. Re: FreeSurfer Mac crash (fsbuild)
   3. help (Sarah Lavelle)
   4. Re: help (Fischl, Bruce R.,PHD)
   5. MRI recon-all failed at talairach (Jonany, Vincent Joe)


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Message: 1
Date: Tue, 25 Oct 2022 06:14:54 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Fail to install FreeSurfer 7 from the *.deb
        package
To: freesurfer@nmr.mgh.harvard.edu
Cc: liangqunjun@foxmail.com
Message-ID: <9e9ccbd9762dc3fe12a584cc5905b258@trashmail.com>
Content-Type: text/plain; charset="utf-8"

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This error in the log reports the file is likely corrupted and so could not be unpacked and installed,



    dpkg-deb (subprocess): decompressing archive member: lzma error: compressed data

&nbsp;is corrupt

The md5 checksum of the file
downloaded to your machine needs to match the MD5 sum column
for the file as listed on the download page.&nbsp; Check you see the output listed below before trying to install the .pkg file (and re-download if necessary).

- R.


$ md5sum&nbsp; freesurfer_ubuntu20-7.3.2_amd64.deb
b2d0f8e6285f4a8da72d008a6390a7fe&nbsp; freesurfer_ubuntu20-7.3.2_amd64.deb



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Message: 2
Date: Tue, 25 Oct 2022 06:50:27 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] FreeSurfer Mac crash
To: freesurfer@nmr.mgh.harvard.edu
Cc: paryara7@gmail.com
Message-ID: <31fa687912ee8902bf6bd8e7a1c09d22@trashmail.com>
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Try running the commands below in a new terminal window. &nbsp;You can run the bash shell and set the environment variable FS_LICENSE to point to the license.txt file you downloaded after filling out the form,&nbsp;https://secure-web.cisco.com/1IL6-bXyqY3LwkwCeLHW8BrasqmSMK-CMfKLENH2RSpuWz2skzo24rSpe3Ucq8BVCOBYACh4N8UMh68nfQH-kQzZKeO_QiY9TalAYOO4QG_uvFBCRRwI7_71e5EW_QnP1Uc9tAXRy8hYZUMKFpbslZfvJzkIWiPSSC3uZWa4EWYZyZpPXPM_xlhTvswpg_LmhysnNZZ8Hmqbg4P-IGq_bhTP_8ShhIwZBjq-T6ceQc4UDxST-OGVyX53MZnNkaLnIH8QDhRAI7AfMtJtQCstlmFGa4BxS1uilWjfCILMWzNPbstJAsi93GZZzPUdyseac/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp; &nbsp;I used an Intel Mac below, but it should work if you are on a newer Mac with the M1 or M2 chip.
- R.
- - - - - - -
iMac:~ myuserid$ bashThe 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/1q1PYonuAvBGkY2sdlfWfdq5vkeftncQHnhJhoCzvdI_yrKRjWD4suxAPLaWosP4gmZPq_nsAU4XwdQZO5onmSzYq7uVjVyhtxzXYtN-fK4p_MAamRnOYTZMd5Z1FU3g6CGZnC_lWjVtJZEReoXfUkOoQvPPFXRuK8E3hdGspQKp6I2YZ8eWpG4KeWZTsoK0MSGlUgoVpbM0tW4PUsPZKmUL8pMBFFZnwDUFw9xMu2bLrikZ-4FAyx59LrmxpQvsK_nl80gTARF360eOKUtvvHCephnR6E8OyM6LG1FfIUAj3lgXclL93xuO70-QDtYaT/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050.iMac%3A%7E%24 sw_versProductName:  macOSProductVersion:    12.6&nbsp;&nbsp;&lt;-- RUNNING MAC OS 12.6 &nbsp;(ON AN INTEL MAC)BuildVersion: 21G115iMac:~$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
iMac:~$ source /Applications/freesurfer/7.3.2/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME&nbsp;&nbsp;&nbsp;/Applications/freesurfer/7.3.2
FSFAST_HOME&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.3.2/subjects
MNI_DIR&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.3.2/mni

iMac:~$ pwd
/Users/myuserid
iMac:~$ echo $HOME
/Users/myuserid
iMac:~$ ls license.txt
license.txt
iMac:~$ export FS_LICENSE=$HOME/license.txt

iMac:~$ which freeview
/Applications/freesurfer/7.3.2/bin/freeview

iMac:~$ freeview&nbsp;&nbsp;    &lt;-- SHOULD OPEN AN EMPTY FREEVIEW WINDOW

iMac:~$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz&nbsp;&nbsp;   &lt;-- SHOULD DISPLAY KNOWN TO BE GOOD VOLUME FILE

On Oct 23, 2022, at 12:29, Parya Rahimi &lt;paryara7@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello, I recently downloaded freesurfer and when I try to load a volume, the application just crashes and shows me the error I copied below. Please let me know how to fix this. Thank youRegards,Parya Rahimi
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Message: 3
Date: Tue, 25 Oct 2022 10:29:53 +0100
From: Sarah Lavelle <lavells1@tcd.ie>
Subject: [Freesurfer] help
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CABRNrkeRPLQWU3tXnZ9CBDvuip1E4pmPPDSizkEt_h4=Kwh4hA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this
https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUxICtX_m72JgFOKgqmcmDmNUv_rPvux5Bj3HvJdGS1wmDMB49Af-BJx9Q5hozmhhuUcgnG8xeUpfoO4g2LSz1OdFi_9on9h5ngyGR9FDKKAgMIOCzYJezDsIESZYkKSRdPHkAWMlYTYYAHYx4iD-JqVc30z2DimXPHyrLEyGpNChw8D4PkkLoasWz2jf7w4Pefp9yJvvDnZx-gyl0BhCk8ul3x-2cGVK0SVa-LKxKQHzToFKqsURPjIXBXX2NOr8s_VgCRqHl8WzMW3bCwJiearZFL1Avboe-CZ8CLgZe_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Flattening but it isn't
enough for the project I am doing. I want to flatten the whole surface but
I may need to change where I am cutting from patient to patient. How do you
know how big the hole should be? and how many relaxation cuts should you
make? How long should they be? If you have any more guidance on how to cut
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal
gives me a % near the end saying "41% total metric distortion". Can you
confirm that this value is the total metric distortion from an inflated
surface to a flatmap surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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Message: 4
Date: Tue, 25 Oct 2022 14:49:14 +0000
From: "Fischl, Bruce R.,PHD" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] help
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM8PR04MB79768CDF98D8D0ECF20502C6EF319@DM8PR04MB7976.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Hi Sarah

Sorry, I?m not sure we have much to add. We don?t flatten much any longer, and the cuts are kind of ad hoc ? the one around the medial wall to get rid of non-cortical stuff, then the radial ones from there to remove particularly the curvature from the 3 poles. Mostly we just follow what Anders and Marty started doing way back when
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Sarah Lavelle
Sent: Tuesday, October 25, 2022 5:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] help


        External Email - Use Caution
Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening<https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUxICtX_m72JgFOKgqmcmDmNUv_rPvux5Bj3HvJdGS1wmDMB49Af-BJx9Q5hozmhhuUcgnG8xeUpfoO4g2LSz1OdFi_9on9h5ngyGR9FDKKAgMIOCzYJezDsIESZYkKSRdPHkAWMlYTYYAHYx4iD-JqVc30z2DimXPHyrLEyGpNChw8D4PkkLoasWz2jf7w4Pefp9yJvvDnZx-gyl0BhCk8ul3x-2cGVK0SVa-LKxKQHzToFKqsURPjIXBXX2NOr8s_VgCRqHl8WzMW3bCwJiearZFL1Avboe-CZ8CLgZe_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Flattening> but it isn't enough for the project I am doing. I want to flatten the whole surface but I may need to change where I am cutting from patient to patient. How do you know how big the hole should be? and how many relaxation cuts should you make? How long should they be? If you have any more guidance on how to cut to mini
 mise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal gives me a % near the end saying "41% total metric distortion". Can you confirm that this value is the total metric distortion from an inflated surface to a flatmap surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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Message: 5
Date: Tue, 25 Oct 2022 15:49:20 +0000
From: "Jonany, Vincent Joe" <vincent.jonany@charite.de>
Subject: [Freesurfer] MRI recon-all failed at talairach
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <33a65781-0e4b-42af-82e2-692c783c3527@Spark>
Content-Type: text/plain; charset="utf-8"

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Dear FreeSurfer Developers,

I am encountering a weird error in performing recon-all in my dicom directory. I believe the problem is here (snippet copied from talairach_avi.log. I have also attached here the recon-all.log, as well as the talaraich_avi.log. Does anyone know or have seen this problem before? I will appreciate any kind of help, please let me know if I need to provide anything else.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: MacOS Monterey (apple silicon)

$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
256 256 256 1
1.000000 1.000000 1.000000
orientation T byte_order littleendian
Reading image: /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
dimensions: 256 256 256
mmppix: 1.0000 -1.0000 -1.0000
center: 128.0000 -129.0000 -129.0000
talsrcimg_g11.4dfp.img
256 256 256 1
1.000000 1.000000 1.000000
orientation T byte_order littleendian
Reading image: talsrcimg_g11.4dfp.img
dimensions: 256 256 256
mmppix: 1.0000 -1.0000 -1.0000
center: 128.0000 -129.0000 -129.0000
t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupu??N
?E???????7S?0??N
#??>?x?N
??N
??N
S???N

?N
?@
??N
?
? read error
t4_read: transform initialized to I4
rotation matrix determinant 1.000000

Thank you in advance! I appreciate any help!

Best,

Vincent
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End of Freesurfer Digest, Vol 224, Issue 32
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