Re: [Freesurfer] Pial and White surface maps are not found

2023-07-20 Thread fsbuild 
External Email - Use Caution

 Hello Varun,
The Windows file system, i.e., NTFS, does not support soft links.  So you 
cannot set SUBJECTS_DIR to storage mounted from your Windows machine that has 
been formatted by Windows OS, and then run something in the linux VM that is 
going to try to write and create a soft link there, e.g., if that is 
what /media/sf_VBOX/T1_FreeSurfer is set to point to via SUBJECTS_DIR. 
  Anything that writes and creates a soft link running in the 
linux VM needs to write directly to the linux file system inside the VM.
- R.
On Jun 21, 2023, at 11:55, Varun Chandran <varunchandra...@gmail.com> 
wrote:External Email - Use 
Cautionp.s. I am wondering 
whether this specific issue arises while working with freesurfer using Linux 
based Virtual Machine? On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran 
<varunchandra...@gmail.com> wrote:Hi  YujingThank you very much 
for your quick reply. Yes, I used a directory path to set an environment 
variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the 
'recon-all' command line. However, it was not very helpful to obtain the pial 
and white surface maps and exited with some errors as shown in the 
recon-all.log (please see the file attached). Now, I'll try running the same 
command by entering the full path name of the directory as you suggested.  
                      
                      
                      
                      
                      
                 thanks 
again,best,VarunOn Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing 
<yhuan...@mgh.harvard.edu> 
wrote:External Email - Use 
CautionHi Varun, I’m not 
sure what issue that you have been running into. Can you send your 
recon-all.log? In general, you need to1. set environment variable 
SUBJECTS_DIR to some directory that you have write permission2. pass full path 
to T1 image to -i 
<full_path_to_T1_image> Best, Yujing  From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On
 Behalf Of Varun ChandranSent: Wednesday, June 21, 2023 10:32 
AMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Pial and White 
surface maps are not 
found External Email - Use 
CautionHi FS experts, It's 
been a few years, I used FS tools for cortical surface reconstruction. Now, 
when I used the freesurfer 7.2 version to perform cortical surface 
reconstruction on the T1-weighted structural MRI data, I was unable to obtain 
the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some 
light on this issue? command line used: recon-all -s T1_260423 -i 
T1_260423 -all -qcache              
                      
                      
    thanks, best,Varun -- Varun Arunachalam Chandran, 
PhDPostdoctoral Research Associate,Faculty of biology, medicine and 
health,School of health sciences,University of Manchester,United 
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Re: [Freesurfer] Pial and White surface maps are not found

2023-07-20 Thread Douglas N. Greve 
   External Email - Use Caution

recon-all died immediately after trying to create a symlink. Might be 
because it is on a VBox. Rob, can you help figure this out?


On 6/21/2023 11:55 AM, Varun Chandran wrote:


External Email - Use Caution

p.s. I am wondering whether this specific issue arises while working 
with freesurfer using Linux based Virtual Machine?


On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran 
 wrote:


Hi Yujing

Thank you very much for your quick reply. Yes, I used a directory
path to set an environment variable
(SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the
'recon-all' command line. However, it was not very helpful to
obtain the pial and white surface maps and exited with some errors
as shown in the recon-all.log (please see the file attached). Now,
I'll try running the same command by entering the full path name
of the directory as you suggested.

               thanks again,

best,
Varun


On Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing
 wrote:

External Email - Use Caution

Hi Varun,

I’m not sure what issue that you have been running into. Can
you send your recon-all.log?

In general, you need to

1. set environment variable SUBJECTS_DIR to some directory
that you have write permission

2. pass full path to T1 image to -i 

Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of *Varun
Chandran
*Sent:* Wednesday, June 21, 2023 10:32 AM
*To:* Freesurfer support list 
    *Subject:* [Freesurfer] Pial and White surface maps are not found

*External Email - Use Caution *

Hi FS experts,

It's been a few years, I used FS tools for cortical surface
reconstruction. Now, when I used the freesurfer 7.2 version
to perform cortical surface reconstruction on the T1-weighted
structural MRI data, I was unable to obtain the lh/rh.pial and
lh/rh.white surface maps. Can anyone please shed some light on
this issue?

command line used: recon-all -s T1_260423 -i T1_260423 -all
-qcache

                                  thanks,

best,

Varun

-- 


Varun Arunachalam Chandran, PhD

Postdoctoral Research Associate,

Faculty of biology, medicine and health,

School of health sciences,

University of Manchester,

United Kingdom.

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Re: [Freesurfer] Pial and White surface maps are not found

2023-06-21 Thread Varun Chandran 
External Email - Use Caution

p.s. I am wondering whether this specific issue arises while working with
freesurfer using Linux based Virtual Machine?

On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran 
wrote:

> Hi  Yujing
>
> Thank you very much for your quick reply. Yes, I used a directory path to
> set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer)
> before running the 'recon-all' command line. However, it was not very
> helpful to obtain the pial and white surface maps and exited with some
> errors as shown in the recon-all.log (please see the file attached). Now,
> I'll try running the same command by entering the full path name of the
> directory as you suggested.
>
>
>thanks again,
>
> best,
> Varun
>
>
> On Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Varun,
>>
>>
>>
>> I’m not sure what issue that you have been running into. Can you send
>> your recon-all.log?
>>
>>
>>
>> In general, you need to
>>
>> 1. set environment variable SUBJECTS_DIR to some directory that you have
>> write permission
>>
>> 2. pass full path to T1 image to -i 
>>
>>
>>
>> Best,
>>
>>
>>
>> Yujing
>>
>>
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Varun Chandran
>> *Sent:* Wednesday, June 21, 2023 10:32 AM
>> *To:* Freesurfer support list 
>> *Subject:* [Freesurfer] Pial and White surface maps are not found
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi FS experts,
>>
>>
>>
>> It's been a few years, I used FS tools for cortical surface
>> reconstruction. Now, when I used the freesurfer 7.2 version to perform
>> cortical surface reconstruction on the T1-weighted structural MRI data, I
>> was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can
>> anyone please shed some light on this issue?
>>
>>
>>
>> command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache
>>
>>
>>
>>
>>
>> thanks,
>>
>>
>>
>> best,
>>
>> Varun
>>
>>
>>
>> --
>>
>> Varun Arunachalam Chandran, PhD
>>
>> Postdoctoral Research Associate,
>>
>> Faculty of biology, medicine and health,
>>
>> School of health sciences,
>>
>> University of Manchester,
>>
>> United Kingdom.
>>
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/135dxZwIDQx9bbQ4IxE4063rhuKY-x_fftMMGZfTGtSk_plGZ6LdWEv2ZMYt12IvB3X2dI7Kj8GttX9kMCJBp1qi4SdxkH58VOdWyEUMZx_c6mif50a07j64w0R7sSbKh9Yz4luxB1LEyouFCqruu_ewvGQ09MSvAxdD3bcMqOQqd9zKhKdocmm8HHarkeiHKYmbw5oHd3fXo6iiyNpG1VBo1KeB_FWPlPhXBs9ZoGZyVSNDgTrQA0ah4vMbVlU5pRVaCEdzDrs-aeWGPyJkonK3DxaJ24pxim5jWIwVwsIC3STskjz0hJrrHItjGKlb50sYyUgkrwNBVzcJG56MXyA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F
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Re: [Freesurfer] Pial and White surface maps are not found

2023-06-21 Thread Huang, Yujing 
External Email - Use Caution

Hi Varun,

I’m not sure what issue that you have been running into. Can you send your 
recon-all.log?

In general, you need to
1. set environment variable SUBJECTS_DIR to some directory that you have write 
permission
2. pass full path to T1 image to -i 

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Varun Chandran
Sent: Wednesday, June 21, 2023 10:32 AM
To: Freesurfer support list 
Subject: [Freesurfer] Pial and White surface maps are not found


External Email - Use Caution
Hi FS experts,

It's been a few years, I used FS tools for cortical surface reconstruction. 
Now, when I used the freesurfer 7.2 version to perform cortical surface 
reconstruction on the T1-weighted structural MRI data, I was unable to obtain 
the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light 
on this issue?

command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache


thanks,

best,
Varun

--
Varun Arunachalam Chandran, PhD
Postdoctoral Research Associate,
Faculty of biology, medicine and health,
School of health sciences,
University of Manchester,
United Kingdom.
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[Freesurfer] Pial and White surface maps are not found

2023-06-21 Thread Varun Chandran 
External Email - Use Caution

Hi FS experts,

It's been a few years, I used FS tools for cortical surface reconstruction.
Now, when I used the freesurfer 7.2 version to perform cortical surface
reconstruction on the T1-weighted structural MRI data, I was unable to
obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please
shed some light on this issue?

command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache


thanks,

best,
Varun

-- 

Varun Arunachalam Chandran, PhD

Postdoctoral Research Associate,

Faculty of biology, medicine and health,

School of health sciences,

University of Manchester,

United Kingdom.

https://secure-web.cisco.com/1cnuenNM09eOjp8mrBzh-QGzKlgQQ0c8Rw7bNumyV-qFdkCjJPaU7LXYRxKGgbYxUiRXi5zKScT5gHmVubIUvIUpsPPuJKYBPYb_HvYI02KUmRTUjZN_AtsagwYGP1pqFwfThhqJzeoAwW5vW-rIS2c23JlIQc8TSb27qeu7ZKdzERpB1pZzxuqUfgJuv4jA0o3BBdnDICJEgOPcUcYjbYS5eLXVgmkvLtU-PoHVJRjCAiH-vUxn3hP6EAhuIxa7DOtcbhEy2VZVoF5ADRqVWhwvxjs7pXFwpB5rA8kzvx97Uh4_4nLhM1JhURLJWtUxl4THj_dQ2B6bNbuyayXzQLw/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F
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 .
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