date:20230703

Re: [Freesurfer] dcmunpack: Issues with the -run argument

2023-07-03 Thread Sara Teso Cuesta

External Email - Use Caution

You are right, I see 'Found 2 unique series: 9 11' and it works with both
of the numbers. I assume I have to do this with every single series in the
data, am I correct? Is there a way to do this automatically avoiding
specifying the series in each command execution?

Thank you so much for you help,

S

El lun, 3 jul 2023 a las 20:05, Huang, Yujing ()
escribió:

> External Email - Use Caution
>
> dcmunpack -src-targ  -fsfast -run 
>   
>
>
>
> 1. specify full path to your dicom directory for ‘-src ’
>
> 2. specify full path for ‘-targ ’, or it will be created under
> the directory where you ran dcmunpack
>
> 3. I think you should see ‘Found 18 unique series: 1 2 …’ in the output. I
> believe  should be one of these series Nos.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sara Teso Cuesta
> *Sent:* Friday, June 30, 2023 1:05 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] dcmunpack: Issues with the -run argument
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
>
>
> I am trying to use dcmunpack to transform dicom images to a nifti format
> inside a FSFAST formatted directory (*MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1WAmqtiZcIFFODzsU2EP85wir6ZmWS21-nINNOBJjVaZr_qcdpl0UaSak42yFXn_DDQX0zsOMLOIuEoxCfNSVinNrMRWygzVKoaiMzSF8v5TulKODlx33WewCNEHLCCdBgZhQsaih--NwJ9QdG2Rpuzo0rKCmQ8yvP0iL9G8GIHXJBWNeiT_Pd273nWMjIG3OFmCwpdv5NuA-GtEmdvcPx0eqCzXH66AQTVsaJKIXWWIZh0XiiIo2lLVTf9XOAi4xj1kvElkHFQU7huHCL1oq2PRLqYuGr_0A4eCNCMOZ1vB7mvRXw4wqqhRyHJeD8pPY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ffsfastrestingstatetutorial
> ),
> however I am having issues understanding how to use properly the -run
> argument.
>
>
>
> This is the command I am trying to use:
>
>
>
> dcmunpack -src  fMRI_dir  -targ sessionid -fsfast -run 2 rest nii.gz
> f.nii.gz
>
>
>
> I assume I am making some mistakes with the command, specially with the
> run arguments since this is the error that I got in the terminal: ERROR:
> could not find run 2 in data
>
>
> My directory contains fMRIs downloaded directly from the ADNI database and
> grouped in folders following this structure:
>
> /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images
>
> I've searched the list and no similar errors have been reported. Does
> anyone have any thoughts on how to solve this?
>
> 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb
> 2) Platform: Ubuntu 20.04 in WSL
>
>
>
> Thanks for your help.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> Brigham Compliance HelpLine at
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>  <
> https://secure-web.cisco.com/1Ot5E7mJ4euWEHrVtS6u9WkdgGKXOXghAzkPRbHjv6kNkmAiLNMQ_pRemOoo1g19cptRvOXrsJwafVf_u0gThQ3jvUx6QZNOw2u2svT16f9Vlwe37Aiet7rVB0FhKZ_-DGbrM7xLiRQ_iLu5hS9nZZBN9D6mASifHmXBgpLpxpKO4z-mxlU5aLuueSgwCSpJp7g876kgaSNt7kfxAThyYgwHV8xvzl1QAY3-MEWAV9wFPlmQoQhkCNrc7u5Ppa5edAf4WtIpDGJkINylviLc-yBRUWxhxjUYNM_Pj3fML8y9oJvHo06VUyYpuY8Qtmw_V/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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Re: [Freesurfer] dcmunpack: Issues with the -run argument

2023-07-03 Thread Sara Teso Cuesta

External Email - Use Caution

You are right, I see 'Found 2 unique series: 9 11' and it works with both
of the numbers. I assume I have to do this with every single series in the
data, am I correct? Is there a way to do this automatically avoiding
specifying the series in each command execution?

Thank you so much for you help,

S

El lun, 3 jul 2023 a las 20:05, Huang, Yujing ()
escribió:

> External Email - Use Caution
>
> dcmunpack -src-targ  -fsfast -run 
>   
>
>
>
> 1. specify full path to your dicom directory for ‘-src ’
>
> 2. specify full path for ‘-targ ’, or it will be created under
> the directory where you ran dcmunpack
>
> 3. I think you should see ‘Found 18 unique series: 1 2 …’ in the output. I
> believe  should be one of these series Nos.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sara Teso Cuesta
> *Sent:* Friday, June 30, 2023 1:05 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] dcmunpack: Issues with the -run argument
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
>
>
> I am trying to use dcmunpack to transform dicom images to a nifti format
> inside a FSFAST formatted directory (*MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/10RhbaiY2D2ZY_bRli2ryVF5Xi3d8Dc24G2wkWrqQzyxALXmO4HuNbQMFtURi1_3ARLrMR2D9hBjlrK_ZsUTPfgfG_uQJGKqLp9Zw0wJjMiKapWrIZf-qbeCnbVntJgXd-9fJayIkNNn70dFG17LEjv26Wij73WYUg3xBeHYFrqQJ0JGjL6DeJ0V0uwJ8dMtilIMBpsBBy5_IiXFIigo8W49wji05ZDD0rB0CPPLwaHzj1X0CX-TmyDGgiZfOKZ1YAupILWkQ8JLNGVdultl5CALg1ReCrYEWUVGZXfGDQ_SexLNBKEbj4FWSmgLL8lKziO5apRJpCEkvBAvQTWjssQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ffsfastrestingstatetutorial
> ),
> however I am having issues understanding how to use properly the -run
> argument.
>
>
>
> This is the command I am trying to use:
>
>
>
> dcmunpack -src  fMRI_dir  -targ sessionid -fsfast -run 2 rest nii.gz
> f.nii.gz
>
>
>
> I assume I am making some mistakes with the command, specially with the
> run arguments since this is the error that I got in the terminal: ERROR:
> could not find run 2 in data
>
>
> My directory contains fMRIs downloaded directly from the ADNI database and
> grouped in folders following this structure:
>
> /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images
>
> I've searched the list and no similar errors have been reported. Does
> anyone have any thoughts on how to solve this?
>
> 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb
> 2) Platform: Ubuntu 20.04 in WSL
>
>
>
> Thanks for your help.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> The information in this e-mail is intended only for the person to whom it
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> Brigham Compliance HelpLine at
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>  <
> https://secure-web.cisco.com/1h7xmUYKT2FWsF5tnb8-ikNRW-_KhCPgml1oWMQ6ywvZQ6t9u78SG39m-DwXuG6wnbAMkc5KHfnluB9ZAz20pM1m-ypfLIf37VYapjDuV-3_p8lCrGtuG47u5s2CyZ2nQnkTFcf8_g_J2vsJvezgH0Y5SsWPGL0DfeIYQaPa7Og8d1Pg5XqpJh7c98s17ZvokGRa4esWuXr6KYhX1zKG8qMI0gYzkUJBAav2-awciiGsLmWFQmE8GG6Km-xMJmBnXTxag1fQjoVfuBFIWK_S0RnbQtL3rONbqNn6n8r9D_TxGZJE5JE1FcDwXAgkjSXsAoEuuy0CcKbarRvShhhfTOQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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[Freesurfer] unsubscribing from mailing list

2023-07-03 Thread Rana Ghamari

External Email - Use Caution

Hi Freesurfer Team

Please unsubscribe my email from the list
Email: ghamarir...@gmail.com


Thanks
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[Freesurfer] mri_segstats dimension mistach

2023-07-03 Thread Fahad Hannan

External Email - Use Caution

Hello,

I'm trying to run the mri_segstats on different input volume. The input volume 
has the same dimensions as the original volume used to perform recon-all. 
However, when trying to use the following command:

"mri_segstats --seg $SUBJECTS_DIR/P6V1/mri/wmparc.mgz --sum 
$SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 
3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm 
--in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt"

I get a dimension mismatch error:

ERROR: dimension mismatch between input volume and seg
  input 112 112 80
  seg   256 256 256

Seems like during the recon-all process, freesurfer changed the dimensions of 
the segmentation file to 256 256 256. Is there a way I can resample the 
segmentation file to the input files dimensions, I know I can resample the 
input to the norm.mgz file but I do not want to tamper with the input file.

Thanks,
Fahad
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Re: [Freesurfer] dcmunpack: Issues with the -run argument

2023-07-03 Thread Huang, Yujing

External Email - Use Caution

dcmunpack -src-targ  -fsfast -run  
  

1. specify full path to your dicom directory for ‘-src ’
2. specify full path for ‘-targ ’, or it will be created under the 
directory where you ran dcmunpack
3. I think you should see ‘Found 18 unique series: 1 2 …’ in the output. I 
believe  should be one of these series Nos.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sara Teso Cuesta
Sent: Friday, June 30, 2023 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dcmunpack: Issues with the -run argument


External Email - Use Caution
Hello FreeSurfer Developers,

I am trying to use dcmunpack to transform dicom images to a nifti format inside 
a FSFAST formatted directory (MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1CywVqXMzceQFTijFiAGI2oBpgf24zhpwtOuCUVK-ju3j3wa92HcLFk4dO_h1kG-5soqsvt1NIYDpdSNT1ux1pIAQRgIKQbDNOxfuLlqsoJImCc6xvfWtK54LiowRgWYHalkJr56eFRCnyBaQU-Vyg40utb19Gl1wkYp7WeTcd1P1a8GITSl-f9NGBYxjAqXndEdy6T3DOsv-DSAFGJQ8JU-gQNMcUB-lAl6MdQTl9EDKR3XddcVyGfxjTb42h2YpcO5kKwLRdvk0rTq1meCPTw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ffsfastrestingstatetutorial),
 however I am having issues understanding how to use properly the -run argument.

This is the command I am trying to use:

dcmunpack -src  fMRI_dir  -targ sessionid -fsfast -run 2 rest nii.gz f.nii.gz

I assume I am making some mistakes with the command, specially with the run 
arguments since this is the error that I got in the terminal: ERROR: could not 
find run 2 in data

My directory contains fMRIs downloaded directly from the ADNI database and 
grouped in folders following this structure:

/fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images

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

1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb
2) Platform: Ubuntu 20.04 in WSL

Thanks for your help.
___
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Re: [Freesurfer] Asymmetry analysis

2023-07-03 Thread Carlos Alcocer

External Email - Use Caution

Thank you. I guess I am still confused on how to actually get results to
visualize. I would like to assess left-right hemispheric cortical asymmetry
. Ideally, i would like the analysis to be paired (ie. L vs R for each
subject, rather than the average of L vs average of R across subjects). How
would I go about analyzing and visualizing this in freesurfer using
xhemi. Also is there a way to this with a ROI rather than the whole brain?

Thanks,

Carlos

On Tue, Jun 20, 2023 at 9:26 AM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> That map is whatever you are studying. Eg, lh.thickness
>
> On 5/25/2023 1:30 PM, Carlos Alcocer wrote:
>
> External Email - Use Caution
> Hello,
>
> I am trying to do an asymmetry analysis using steps detailed in *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* 
> https://secure-web.cisco.com/1_yNnJ9fMi64wWs9Ha4WPhzOEIiP_nSgP3fNcqEdlPAUTHBsMormRtH1uG7T4xSV4GYb3fuvVu9HPdEeEcoLi7p4OX6TiXtjcba8MO0vbTMWhRoATdv7gJo5go_xcxF5BofFGAHkEGU2MQVoUTW1iMNROeneLdTxINLgvUVYJ5PJxittYfUIATJLBwd6KcTTR02GGhXKniBllSqVJRxrOqJe5P0so_97JPwLiaeR6-cOS4jGGmm0YgLa0S9yMyQOACu-JQGfuO3K8oExEMIw78330TuXBdcdeRX1aHB0vrLhMM_febq4aiKTW5u0gj4EA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FXhemi
> 
>
> However, step 1.3 starts with running:
>
> mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh
> --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg
> $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg
>
> What is this lh.map.mgh file? and where can I find it/how can i make it?
>
> Thank you,
>
> Carlos
>
>
>
>
> ___
> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
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Re: [Freesurfer] Error Help

2023-07-03 Thread Misque Boswell

External Email - Use Caution

Yup, That solved it!
Thank you for your help! I totally missed that. 
Misque 

> On Jul 3, 2023, at 9:36 AM, Huang, Yujing  wrote:
> 
> External Email - Use Caution
> 
> 
> lta_convert looks fine in /Applications/freesurfer/7.4.1/.
>  
> Your ‘export FREESURFER_HOME=Applications/freesurfer/7.4.1’ doesn’t have the 
> leading ‘/’.
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > On Behalf Of Misque Boswell
> Sent: Monday, July 3, 2023 12:30 PM
> To: Freesurfer support list  >
> Subject: Re: [Freesurfer] Error Help
>  
> External Email - Use Caution
> 
> Thank you, Yujing. Here it is:
>  
> Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 
> 7.4.1
>  
> ProgramName: lta_convert  ProgramArguments: 
> /Applications/freesurfer/7.4.1/bin/lta_convert -all-info  ProgramVersion: 
> 7.4.1  TimeStamp: 2023/07/03-16:28:36-GMT  BuildTime: Jun 14 2023 00:15:19  
> BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: 
> misqueboswell  Machine: Misques-MBP-3.local  Platform: Darwin  
> PlatformVersion: 22.2.0  CompilerName: Clang  CompilerVersion: 12.0.0
>  
> Misque 
> 
> 
> On Jul 3, 2023, at 8:55 AM, Huang, Yujing  > wrote:
>  
> External Email - Use Caution
> 
>  
> Can you run the following at prompt?
>  
> ‘Applications/freesurfer/7.4.1/bin/lta_convert -all-info’
>  
> I’m not a Mac user. Do you need ‘/’ in front of ‘Application’?
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > On Behalf Of Misque Boswell
> Sent: Monday, July 3, 2023 11:44 AM
> To: Freesurfer support list  >
> Subject: Re: [Freesurfer] Error Help
>  
> External Email - Use Caution
> 
> Hello Yujing, 
>  
> Thank you for your response. I followed the directions for setup and sourced 
> SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. 
>  
> Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
> Misques-MBP-3 / % 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
> FSL_DIR   /Users/misqueboswell/fsl
>  
>  
> Can you check where your recon-all is and if lta_convert is in the 
> distribution?
> 1. which recon-all
>  
> Misques-MBP-3 / % which recon-all
> Applications/freesurfer/7.4.1/bin/recon-all
>  
> 2. ls -l /lta_convert
>  
> lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" 
> (rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert) 
>  
> Thank you again for your help! 
> Misque 
> 
> 
> 
> On Jul 3, 2023, at 6:26 AM, Huang, Yujing  > wrote:
>  
> Yujing
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
> claiming to 
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>  
> 
>  
> The information in this e-mail is intended only for

Re: [Freesurfer] Error Help

2023-07-03 Thread Huang, Yujing

External Email - Use Caution

lta_convert looks fine in /Applications/freesurfer/7.4.1/.

Your ‘export FREESURFER_HOME=Applications/freesurfer/7.4.1’ doesn’t have the 
leading ‘/’.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Misque Boswell
Sent: Monday, July 3, 2023 12:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error Help


External Email - Use Caution
Thank you, Yujing. Here it is:

Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info
7.4.1

ProgramName: lta_convert  ProgramArguments: 
/Applications/freesurfer/7.4.1/bin/lta_convert -all-info  ProgramVersion: 7.4.1 
 TimeStamp: 2023/07/03-16:28:36-GMT  BuildTime: Jun 14 2023 00:15:19  
BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: 
misqueboswell  Machine: Misques-MBP-3.local  Platform: Darwin  PlatformVersion: 
22.2.0  CompilerName: Clang  CompilerVersion: 12.0.0

Misque


On Jul 3, 2023, at 8:55 AM, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:


External Email - Use Caution

Can you run the following at prompt?

‘Applications/freesurfer/7.4.1/bin/lta_convert -all-info’

I’m not a Mac user. Do you need ‘/’ in front of ‘Application’?

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Misque Boswell
Sent: Monday, July 3, 2023 11:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Error Help


External Email - Use Caution
Hello Yujing,

Thank you for your response. I followed the directions for setup and sourced 
SetUpFreeSurfer.sh as you stated. All goes as planned up to this point.

Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
Misques-MBP-3 / % 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
FSL_DIR   /Users/misqueboswell/fsl


Can you check where your recon-all is and if lta_convert is in the distribution?
1. which recon-all

Misques-MBP-3 / % which recon-all
Applications/freesurfer/7.4.1/bin/recon-all

2. ls -l /lta_convert

lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" 
(rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert)

Thank you again for your help!
Misque



On Jul 3, 2023, at 6:26 AM, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Yujing

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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claiming to be 
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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 MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be

Re: [Freesurfer] Error Help

2023-07-03 Thread Misque Boswell

External Email - Use Caution

Thank you, Yujing. Here it is:

Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 
7.4.1

ProgramName: lta_convert  ProgramArguments: 
/Applications/freesurfer/7.4.1/bin/lta_convert -all-info  ProgramVersion: 7.4.1 
 TimeStamp: 2023/07/03-16:28:36-GMT  BuildTime: Jun 14 2023 00:15:19  
BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: 
misqueboswell  Machine: Misques-MBP-3.local  Platform: Darwin  PlatformVersion: 
22.2.0  CompilerName: Clang  CompilerVersion: 12.0.0

Misque 

> On Jul 3, 2023, at 8:55 AM, Huang, Yujing  wrote:
> 
> External Email - Use Caution
> 
> 
> Can you run the following at prompt?
>  
> ‘Applications/freesurfer/7.4.1/bin/lta_convert -all-info’
>  
> I’m not a Mac user. Do you need ‘/’ in front of ‘Application’?
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > On Behalf Of Misque Boswell
> Sent: Monday, July 3, 2023 11:44 AM
> To: Freesurfer support list  >
> Subject: Re: [Freesurfer] Error Help
>  
> External Email - Use Caution
> 
> Hello Yujing, 
>  
> Thank you for your response. I followed the directions for setup and sourced 
> SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. 
>  
> Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
> Misques-MBP-3 / % 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
> FSL_DIR   /Users/misqueboswell/fsl
>  
>  
> Can you check where your recon-all is and if lta_convert is in the 
> distribution?
> 1. which recon-all
>  
> Misques-MBP-3 / % which recon-all
> Applications/freesurfer/7.4.1/bin/recon-all
>  
> 2. ls -l /lta_convert
>  
> lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" 
> (rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert) 
>  
> Thank you again for your help! 
> Misque 
> 
> 
> On Jul 3, 2023, at 6:26 AM, Huang, Yujing  > wrote:
>  
> Yujing
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
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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 
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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

Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits

2023-07-03 Thread Huang, Yujing

External Email - Use Caution

With '-autorecon2-noaseg -autorecon3', I believe aseg.mgz is re-created.  So, 
aseg.stats should reflect the changes.

I'm not sure cortex.label is re-created with these two options.  So, not sure 
about ?h.aparc.stats.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Alexopoulos, Dimitrios
Sent: Thursday, June 29, 2023 4:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits


External Email - Use Caution
A few quick questions FS experts.

I made manual edits on subcortical structures in outputs from FS6.0. 
Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using:
recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3

Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these 
changes?

I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz


# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil



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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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immediately notify the sender via telephone or return mail.
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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] Error Help

2023-07-03 Thread Huang, Yujing

External Email - Use Caution

Can you run the following at prompt?

'Applications/freesurfer/7.4.1/bin/lta_convert -all-info'

I'm not a Mac user. Do you need '/' in front of 'Application'?

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Misque Boswell
Sent: Monday, July 3, 2023 11:44 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error Help


External Email - Use Caution
Hello Yujing,

Thank you for your response. I followed the directions for setup and sourced 
SetUpFreeSurfer.sh as you stated. All goes as planned up to this point.

Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
Misques-MBP-3 / % 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
FSL_DIR   /Users/misqueboswell/fsl


Can you check where your recon-all is and if lta_convert is in the distribution?
1. which recon-all

Misques-MBP-3 / % which recon-all
Applications/freesurfer/7.4.1/bin/recon-all

2. ls -l /lta_convert

lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" 
(rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert)

Thank you again for your help!
Misque


On Jul 3, 2023, at 6:26 AM, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Yujing

___
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] Error Help

2023-07-03 Thread Misque Boswell

External Email - Use Caution

Hello Yujing, 

Thank you for your response. I followed the directions for setup and sourced 
SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. 

Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1
Misques-MBP-3 / % 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
FSL_DIR   /Users/misqueboswell/fsl

Can you check where your recon-all is and if lta_convert is in the distribution?
1. which recon-all

Misques-MBP-3 / % which recon-all
Applications/freesurfer/7.4.1/bin/recon-all

2. ls -l /lta_convert

lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" 
(rwxr-xr-x  1 root  wheel   2613752 Jun 13 21:21 lta_convert) 

Thank you again for your help! 
Misque 

> On Jul 3, 2023, at 6:26 AM, Huang, Yujing  wrote:
> 
> Yujing

___
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Re: [Freesurfer] Hippo subfields long

2023-07-03 Thread Iglesias Gonzalez, Juan E.

External Email - Use Caution

Dear Andrei,
The script requires that you’ve run the main FreeSurfer longitudinal pipeline 
(see Longitudinal Processing in the wiki).
Don’t worry about the files, they have different names and can coexist without 
issues 
Cheers,
/E


--
Juan Eugenio Iglesias
http://secure-web.cisco.com/10fTQ42u4_V7tprrGhZtquem9C8ol86QGWI0WSKTeJmrMNbbbBfv6TXMg2qxFleC48s3zH-4u9m5nfjQS7_fKmUn6GkY2oZQkRwX92k2LGnbYgF_waVU7auGmc9AaJyX02KjoIWf9lngiEqNjnRAzHQVFVbuxXlEuDN515b1WjioA5LC96IYogsYAvNT7xnoMaT-_kJw0wnWXkvlLzMnewj7RVJWE0ZyKP6Te_bsblaEFj0_W9B0HtJv3BHbTIaEK09xDOxjj1HFdS6U6mLna4w/http%3A%2F%2Fwww.jeiglesias.com

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

Date: Sunday, July 2, 2023 at 17:27
To: Freesurfer support list 
Subject: [Freesurfer] Hippo subfields long

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Hello everyone,

Quick question.
After running the longitudinal recon-all pipeline, is it required to run all 
subjects/tps through the segmentHA before running the segmentHA_long?
If no, since I already ran the segment_HA in a few subjects, if I stop and 
start running the segmentHA_long, will I have any trouble in overlaying output 
files?

Thank you in advance!
Andrei
--
Andrei Bieger
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Re: [Freesurfer] Error Help

2023-07-03 Thread Huang, Yujing

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Hi Misque,

I see the error in your recon-all.log
“
7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460)
ERROR: Executable 'lta_convert -all-info failed! Is it missing from the 
distribution?'
“

Here is some information on how to set up Freesurfer on Mac - 
https://secure-web.cisco.com/1Wx0z_tw2w2WyPGsxqDZHPgpnq18mkkoGjEO-ae48MqpV3_1StPfPI4r5H7H0hbCbSVNdgcp7PWcKkyT6FlrNn3EFP_Oay79L28d-j6NygNRCf_DFPGdtrJOYmBU5UiYxnG-EcX8aw_JUQImMgA5sOb-hKPWT5mXCVpX79xiILUYGwY3NtVNCci-wP7bMWL8qglsn72H-HXDYgA8Nxw1d6udZhE2KfVGyO94Rv9eYfh1brypJRKE2xNOsTWaO_lTco196JDgT-ql7g5VtYqSFpg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Mac

I’m assuming that you sourced SetUpFreeSurfer.sh from your Freesurfer install 
directory.

Can you check where your recon-all is and if lta_convert is in the distribution?
1. which recon-all
2. ls -l /lta_convert

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Misque Boswell
Sent: Sunday, July 2, 2023 8:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error Help


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Hi,

I am new to FS and recently downloaded the package per instructions on your 
site.
I set up the path and everything seems to be fine until I attempt to use any 
functions.

I have searched for answers on this error, but I cannot seem to find anything 
so I am hoping you can direct me in fixing this.

I am attaching the error log. I also tried to preprocess “bert” and got the 
same message.

Thank you!

Misque

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Re: [Freesurfer] dcmunpack: Issues with the -run argument

Re: [Freesurfer] dcmunpack: Issues with the -run argument

[Freesurfer] unsubscribing from mailing list

[Freesurfer] mri_segstats dimension mistach

Re: [Freesurfer] dcmunpack: Issues with the -run argument

Re: [Freesurfer] Asymmetry analysis

Re: [Freesurfer] Error Help

Re: [Freesurfer] Error Help

Re: [Freesurfer] Error Help

Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits

Re: [Freesurfer] Error Help

Re: [Freesurfer] Error Help

Re: [Freesurfer] Hippo subfields long

Re: [Freesurfer] Error Help

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