Re: [Freesurfer] Scratch Directory Permissions Denied

[fsbuild]

External Email - Use Caution

Is SUBJECTS_DIR for Freesurfer being set to live under a temporary 
scratch directory initially created by and then subsequently used by Matlab?
If so, maybe Freesurfer is deleting files and/or changing file permissions 
there - causing Matlab to subsequently complain. I would not expect 
multiple programs writing to the same directory tree to work together if they 
use different file permissions, privileges, and/or perform independent 
clean/delete functions in shared directories.
- R.

On Jan 9, 2024, at 14:47, Michael Ruvalcaba 
michaelruvalc...@berkeley.edu 
wrote:External Email - Use 
CautionHello,I am trying to run 
the recon -all function in my MATLAB pipelineusing Freesurfer 6.0.0 and I 
haveno issues with it. However, when I run the recon -all step using 
Freesurfer 7.2.0 and run the following command (the recon -all step finishes 
without error by the way):ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);I get the following 
error:/bin/bash: 
/scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission 
deniedThe issue is there is no scratch file and it looks like between version 
6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory 
(which 6.0.0 doesn't)Does anyone have any inputon this? I hope this made 
sense!Best,Michael 
Ruvalcaba___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[fsbuild]

External Email - Use Caution

I would check with your IT support staff about the error including asking 
if the machines in your cluster are setup to display X Windows sessions with 
image viewing applications like Freeview. If the machines support 
remote graphics, they should be able to tell you what you need to set in your 
terminal session for it to work. But it could be they expect 
programs like freeview to run on your local client machine and read the image 
files/data over the network via NFS, etc.
- R.

On Jan 9, 2024, at 18:52, Dong, Yilei yid...@health.ucsd.edu 
wrote:External Email - Use 
CautionDear freesurfer 
help,I have freesurfer installed on UCSD's Expanse HPC, which is on the 
Rocky Linux 8 operating system. Every time I try to open freeview, it always 
keeps aborting. How should I fix this so that freeview's GUI can be shown? I 
have included the screenshot for reference on the error.Thank 
you.Sincerely,YileiScreen Shot 2024-01-09 at 3.47.14 
PM.png___Freesurfer mailing 
listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Freesurfer] Scratch Directory Permissions Denied

[Michael Ruvalcaba]

External Email - Use Caution

Hello,

I am trying to run the recon -all function in my MATLAB pipeline using
Freesurfer 6.0.0 and I have no issues with it. However, when I run the
recon -all step using Freesurfer 7.2.0 and run the following command (the
recon -all step finishes without error by the way):

ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

I get the following error:

/bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh:
Permission denied

The issue is there is no scratch file and it looks like between version
6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch
directory (which 6.0.0 doesn't)

Does anyone have any input on this? I hope this made sense!

Best,
Michael Ruvalcaba
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] [WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error

[Fischl, Bruce R.,PHD]

Do you acquire any other scans, like an mprage, in the same session? If so, the 
easiest thing to do would be to push that through our recon-all pipeline, then 
register your MPF images to either the mprage or to surfaces using bbregister 
and you can transfer whatever parcellations/segmentations you like

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ERNEST KISSI
Sent: Tuesday, January 9, 2024 2:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error


External Email - Use Caution

Dear Freesurfer Developers,

I am a graduate student working on Macromolecular Proton Fraction (MPF) and I 
need to generate parcellation for it using Freesurfer. I have read several 
articles that reported successful results with this method. However, I have 
encountered some errors when I tried to run Freesurfer on my data. Some of the 
errors are related to transformation at the talairach, and some are related to 
missing brain mask. I have been struggling with these issues for four days and 
I have not been able to process any of my data. I have an urgent deadline for 
my thesis presentation on Friday and I would appreciate your assistance.

I have subscribed to the mailing list but I have not received a confirmation 
email yet. I have attached a screenshot of my registration and two examples of 
my T1 MPF images. Could you please test them on your end and let me know what 
the problem is and how to fix it?

Thank you for your time and support.

Sincerely,
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

[Iglesias Gonzalez, Juan E.]

Dear Francesca,
Our method cannot reliably segment these thin/faint structures from clinical 
scans of arbitrary resolution and contrast, which is why they don’t get 
segmented.
If you want to segment the choroid plexus, you could take then intensities 
under the ventricles and split them into cerebrospinal fluid and choroid eg 
with optimal thresholding.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Biondo, Francesca 

Date: Friday, January 5, 2024 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

External Email - Use Caution
Hi,
recon-all generates these volumes, amongst others: “Left-vessel”, 
“Left-choroid-plexus”, “Right-vessel”, “Right-choroid-plexus”
recon-all-clinical does not generate these volumes. Or at least that I am able 
to detect. Any ideas how to extract or calculate them?

Regarding the choroid plexus, would it be correct to use this formula?
Estimated choroid plexus volume (both left and right) = “VentricleChoroidVol” – 
“left lateral ventricle” – “right lateral ventricle”

Thank you very much for your support -
Francesca

___
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] Infant fs

[Amrita Pal]

External Email - Use Caution

Thanks a lot Lilla.

On Tue, Jan 9, 2024, 3:45 AM Zollei, Lilla,Ph.D. 
wrote:

> Hi Amrita,
>
> The download link has been sent to you.
>
> The thalamus does get segmented with infantFS and the LUT is the same as
> for the adult recon. I would process the 11 year old data with the adult
> pipeline.
>
> Lilla
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Amrita Pal <
> palamritaor...@gmail.com>
> *Sent:* Monday, January 8, 2024 7:17 PM
> *To:* fsbuild 
> *Cc:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] Infant fs
>
>
> External Email - Use Caution
>
> Thanks. I had filled out the form. How long do they take to respond? Also
> can I do subcortical thalamic segmentation with it? How is the LUT
> calculated both for infants and adults? Would you recommend an eleven year
> old's data analyzed by regular FS or infant FS?
>
> On Mon, Jan 8, 2024, 6:19 PM fsbuild  wrote:
>
>
> Looks like you need to fill out the request form,
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1zZvah74BWzrjglb0krNL5dM2nDwFTqLzNo6ha7x_qyZJ-3z73_JUOn6bc4P5vbslrAaoGi8dx_muuVjStR-Nav67m4PgrF3oXTJlYX-1I84q_Lh4Pg9KLIHzT0r7Ycjk-rzGfrN_MeZEsNpCCneuyLM-LmeUAbImoG9v1Lx98FjhsK2LwspgjG_jutMAKky2BRCaWKn8aRvuRpxBuAl3q2f5XW45_H10ZwRuqCDeeDUto5Gh7G5DFKOpBN-eOoTnQZvevoAQKiQcCeXsQcuVey7qMqryjGEay9w1zRnyRMS0My_Oh09HED7172Hiv0ofBArRmTmxBoOg4PAlOEiBsQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS
> 
>
> - R.
>
> On Jan 8, 2024, at 18:12, Amrita Pal  wrote:
>
> External Email - Use Caution
>
> Hello
>
> I am trying to use the infant fs for processing my pediatric data. Where
> can I download the package?
>
> Thanks and Regards
> Amrita
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1GFURJ9Z7X9NaQzvbmI2_j1zZXe2ngB9pchfIoSoptvFeF_XTNlAVKYTlFFSwhRADGK6epki3J08riWEJLUQJHqKP4OHSCCGB28deJV9rqq19_IX_FzFjF2RPHXjVUz4q2IyBXNtxdGmlPlwrcHGG9bg23u8i_C7vNdoHZkhnuvDNCLMyw0AgB0BSqpsRUMKYhk6xoIlInJ53d1GKgzIgkkWxN33_CFc9L1ZGTp6buStJZ9ALZqpRaRj6jD_abwALj04s7qA9qqe_DN2LdemXSYCMzuI4VQwj8b3D0g68PkJvuBO-SdqnG4BgbHKmnBGNB1wEVxUXeYNvybqpELO_8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1GFURJ9Z7X9NaQzvbmI2_j1zZXe2ngB9pchfIoSoptvFeF_XTNlAVKYTlFFSwhRADGK6epki3J08riWEJLUQJHqKP4OHSCCGB28deJV9rqq19_IX_FzFjF2RPHXjVUz4q2IyBXNtxdGmlPlwrcHGG9bg23u8i_C7vNdoHZkhnuvDNCLMyw0AgB0BSqpsRUMKYhk6xoIlInJ53d1GKgzIgkkWxN33_CFc9L1ZGTp6buStJZ9ALZqpRaRj6jD_abwALj04s7qA9qqe_DN2LdemXSYCMzuI4VQwj8b3D0g68PkJvuBO-SdqnG4BgbHKmnBGNB1wEVxUXeYNvybqpELO_8A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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://secure-web.cisco.com/1dCbCucpIuVbjSw5GDe6ArYqkkyE-AsR39gVu13gtsufmvhikZhfscF-UPORlwI6sPeZRPG73ZNEi3t9IwPyxV83sFwB29dOu_V9Z0825nB_-jLQ8n4EJR7e5qd4rHJb-RVhWdc6X9XSkHFfLAv6ZNaV3v2La0c6vCczyj-V_8KZU6TmpfaV60Y8-ciQP3KiBHqFcLuuWgQ_LykSSYz51GnWuBChBq4XSDJCEzFoMaxkpudEQjoX23rwcBrasNaj9oJ7M_MuA_QM6qcdRr58pIstHmzrtVJKRcOEhhkQ0uz8vYAuHjIhW3CvVGSSQBR48NsmSyfjju-TrLbvGENYFyw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> 

[Freesurfer] Sample registration question

[Mirsol Choi]

External Email - Use Caution

Hi there Freesurfer,

I am currently using freesurfer to take DTI metrics (FA, MD) from
hippocampal subfields.
At this point of my exploration with freesurfer, I am able to correctly
register the hippocampal subfields and diffusion data, and obtain my FA
values from the subfields. However, this is at the individual subject
level.

I will eventually need to register all of my samples in the same space for
me to do a group analysis. However I am unsure what the order of
registration should be for this process to be feasible.

Does this order seem feasible for accurate analysis?

1) recon-all all of my subjects
2) dt_recon all of my subjects (one of the outputs is a registration file,
which has registered the DTI data to outputs of recon-all)
3) run the hippocampus segmentation command on all subjects
(segmentHA_T1.sh) to obtain hippocampal subfield segmentation
4) register the segmentation file to the FA maps (output of dt_recon) using
vol2subfield command
5) After creating a subfield-FA map for each subject, spatial normalize the
samples onto the same space using *mri_vol2vol*

Thank you so much for taking the time reading my question. If there is a
different method to spatially normalizing my datasets, or if there is a
more optimal order of registration, I'd be happy to hear from you.

Thank you,
M
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] conversion of D-K atlas

[Fischl, Bruce R.,PHD]

Hi Anna

Parcellation is more than just format conversion - you need to map it onto the 
details of an individual subject's anatomy. In addition, the DKT atlas is only 
cortical. If you want subcortical regions in addition you should run recon-all 
as it will produce both.

Cheers
Bruce

From: Arkhipova Anna, MUDr. 
Sent: Tuesday, January 9, 2024 6:14 AM
To: Freesurfer@nmr.mgh.harvard.edu; fischl 
Cc: phlus...@upol.cz
Subject: conversion of D-K atlas


External Email - Use Caution

Dear prof. Fischl,

We would like to kindly ask a question, if there is a way to convert Fressurfer 
Atlas Desikan-Killiany (lh and 
rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file 
for parcellation of our resting-state fMRI data.

Although we have tried script mri_convert, we obtained only cortical regions, 
but we need also subcortical regions. Would it be anyhow possible?

Thank you so much in advance.

Sincerely yours,
Anna Arkhipova, MD

fMRI laboratory
Department of Neurology, Faculty of Medicine and Dentistry
Palacky University and University hospital Olomouc
Czech Republic




___
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] SynthSR for T2-weighted images

[Iglesias Gonzalez, Juan E.]

Dear Hengameh,
Synthesis of T2 and FLAIR images is on the to-do list, and should happen in the 
next couple of months 
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of hmarz...@student.ubc.ca 

Date: Thursday, January 4, 2024 at 4:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] SynthSR for T2-weighted images

External Email - Use Caution
Hello Eugenio,

I wanted to inquire whether you have plans to create a tool for synthesizing 
T2-weighted  low-field MRI images similar to SynthSR, which was developed for 
T1-weighted images.
I'm in need of synthesizing T2-weighted images for Hyperfine, and I'm curious 
if there is a suitable method available for this purpose.


Because, as I understand it, SynthSR transforms T2-weighted images into 
T1-weighted ones, and it is not designed for handling T2-weighted images. Is my 
understanding correct?

Regards
Hengameh
___
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] Infant fs

[Michelangelo Fabbrizzi]

External Email - Use Caution

Dear Lilla,

I posted a similar question some week ago, I quote it here again, I would be 
grateful if you could provide feedback.

Regards,

Mic

From: Michelangelo Fabbrizzi mailto:michef...@gmail.com>>
Date: Wednesday, October 11, 2023 at 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu  
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Sennott, Liam Ricker mailto:lsenn...@mgh.harvard.edu>>
Subject: Use of infantFS and FS in the interval 2 - 4.5 years of age

External Email - Use Caution

Dear FS experts,

 I see it is recommended to use infantFS below 2 years of age, whereas FS has 
been used for 4.5 years and above.
I was wondering what could be used in the interval 2 - 4.5 years of age: which 
are benefits and drawbacks of both?

Thanks, appreciated,

Mic


> Il giorno 9 gen 2024, alle ore 09:45, Zollei, Lilla,Ph.D. 
>  ha scritto:
> 
> Hi Amrita,
> 
> The download link has been sent to you.
> 
> The thalamus does get segmented with infantFS and the LUT is the same as for 
> the adult recon. I would process the 11 year old data with the adult pipeline.
> 
> Lilla
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > on behalf of Amrita Pal 
> mailto:palamritaor...@gmail.com>>
> Sent: Monday, January 8, 2024 7:17 PM
> To: fsbuild mailto:fsbu...@contbay.com>>
> Cc: freesurfer@nmr.mgh.harvard.edu  
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Infant fs
>  
> External Email - Use Caution
> Thanks. I had filled out the form. How long do they take to respond? Also can 
> I do subcortical thalamic segmentation with it? How is the LUT calculated 
> both for infants and adults? Would you recommend an eleven year old's data 
> analyzed by regular FS or infant FS?
> 
> On Mon, Jan 8, 2024, 6:19 PM fsbuild  > wrote:
>  
> Looks like you need to fill out the request form,
> 
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
> claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/infantFS 
> 
> 
> - R.
> 
>> On Jan 8, 2024, at 18:12, Amrita Pal > > wrote:
>> 
>> External Email - Use Caution
>> 
>> Hello
>> 
>> I am trying to use the infant fs for processing my pediatric data. Where can 
>> I download the package?
>> 
>> Thanks and Regards 
>> Amrita
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> MailScanner has detected a possible fraud attempt from 
>> "secure-web.cisco.com" claiming to 
>> behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://secure-web.cisco.com/15HrOQdxTWLpZpmOwvGl6vMGOQHIjwEsR0WcnsiObzRYrg_EB3l9SujTDV3FExqLhOy1KTN3asft-ATWBUBWUiBIXqz79cP1nQWC0BJoThKFOdRNbgyFScDcRgyi7ppGCq5sDck3_sCbj5wo5c2Gkrt1FQJQVcC7kYudGVwzJs3MRLs8YA1VK3dmOw_9wZKdhiMjriAIlDnmjWdHGLr_MFXMbC0DkFPyCe05KRBf3_rq4Jq3kF_hijuBf8tOMosAXvpL6-Jt54Hl82UwlEz6IYN76tylq9PIhlyMmrc3_cfhzrn3v0JmLCKLwDr-ibiyp/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 
> 

[Freesurfer] 回复： Infant fs

[吴宇轩]

External Email - Use Caution

Your e-mail is wrong.



 回复的原邮件 
| 发件人 | Zollei, Lilla,Ph.D. |
| 日期 | 2024年01月09日 16:45 |
| 收件人 | fsbuild、Freesurfer support 
list |
| 抄送至 | |
| 主题 | Re: [Freesurfer] Infant fs |
Hi Amrita,


The download link has been sent to you.


The thalamus does get segmented with infantFS and the LUT is the same as for 
the adult recon. I would process the 11 year old data with the adult pipeline.


Lilla


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

Sent: Monday, January 8, 2024 7:17 PM
To: fsbuild 
Cc:freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Infant fs
 

External Email - Use Caution

Thanks. I had filled out the form. How long do they take to respond? Also can I 
do subcortical thalamic segmentation with it? How is the LUT calculated both 
for infants and adults? Would you recommend an eleven year old's data analyzed 
by regular FS or infant FS?


On Mon, Jan 8, 2024, 6:19 PM fsbuild  wrote:

 
Looks like you need to fill out the request form,


MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1vHBRl3xOCPsCDolzG52nXzhPfSqQsNFdF4scqtk5SOGJpcqkXAXk69fhCrU2uhjVx4vPz-XXTUBih7s__2RrAHlLqVFDH2s0SlrDsZAWNEZWi2RsDuuOrUABEkVOC4RGhnu37aX0rGMjp06xgmDDk-2B2uDbI8XhJ6oMwYjszw1usLUksWyp_MUnqsRl7g8ILg-im1WOsyUKV7d6blCNXDQ42vb2_VBOVy_A4S8b_PkS-2rRcGTWC51vYbJzHDPXsX-QIE3fWdVGX2_ek_il-QPB-cPzTb25rHy4m5iFzm24q90tsnB6vHWwN8qtmA8tnnw8jNFID5NQTNky5pjVwg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS


- R.



On Jan 8, 2024, at 18:12, Amrita Pal  wrote:



External Email - Use Caution



Hello


I am trying to use the infant fs for processing my pediatric data. Where can I 
download the package?


Thanks and Regards 
Amrita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1Wd8Aubjd3Ktsf9xBgN3poCJsvd_-xf2NIPfy3T3fV-do6wt1rYqrPKMERU0bFsVTfc5xH-G1pWL91Sy8hpvE66Sto_kAe9Mc61wgIlurV7MrcEe2ySfvqHV5f-kw9gS_zxUn7tdHcGRHUBLBK04SolZEYAaTTbMs2gJVqJmznosrlgSEY-4JgYv4Gq9bZvpKN4RD2XYaSEB8k9xyFaBIhgOiaxFQYuFn9iWiTxXiJcuBL6yellM6_AYemKXkrvgBzFjMOF4FCexxGgCX7T5qLakKT8uZIMaeQPGFnCnB9IRggTIfiRotxxorVRaD33XGLgQIU-KHglfdaHkSZcVEiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Subject does not have a bstampfile

[吴宇轩]

External Email - Use Caution

Sorry, your e-mail is so much, I don't want to receive your emails anymore, 
please don't send them again. Thanks



 Replied Message 
| From | Huang, Yujing |
| Date | 01/09/2024 05:10 |
| To | Freesurfer support list |
| Cc | |
| Subject | Re: [Freesurfer] Subject does not have a bstampfile |
You need to specify the input files to process. Here is the wiki page for 
recon-all -  
https://secure-web.cisco.com/1YblSyL9heQXiXS2ETUa7tXZ_aiBBEG51iiBG8O7Pd3gCr-eE40iR4p0UwIFQf2iXbBtBP35RbjBC8h3AczjKfQve8lge7v8ev-OLvxkJcy937MxNy6BqCiOjM3ItxN1dRc3vt68EYJ0h0FTVgIRzmvny75Pxhn_8L3jSAv5MZ3Ns837XT3UHvpZZYQ-jy_-pnPQRIiGqi2CYC-NNVfYhj1wnIo9J0kmpdLG5SueaNDX0SkkN8Ojq85m30rIzjl-iap2zTOo8j_QtBBOSXbpvlpqqfjQqym8T6usyR0px3gogwaioHiyxsp5IiTHkCxXf/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

Best,

Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Joanna Kidon
Sent: Monday, January 8, 2024 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Subject does not have a bstampfile

   External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute Segmentation of hippocampal subfields and nuclei of 
the amygdala (cross-sectional and longitudinal), as described on the 
https://secure-web.cisco.com/1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala,
but I get the following error when I run the recon-all -all -s command:

Subject does not have a bstampfile, copying 
/usr/local/freesurfer/7.3.2/build-stamp.txt
Subject FS Version:
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version Done
INFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME 
/usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 
SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
#
#@# MotionCor Sun Jan  7 20:48:46 CET 2024
ERROR: no run data found in
/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 
001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: 
http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfoUeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9Tjvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1TXcVwnrmkcLYG8z3GWHohA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024




I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one? Also, Ive attached the 
scripts/recon-all.log in case it's of any use.

Best regards,

Joanna


--
--
dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji 
Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii 
Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet 
Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. 
Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej 
Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w Katowicach

PhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic 
Imaging Section of the Polish Society of Medical Physics Department of Invasive 
Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical 
University of Silesia in Katowice Head of the Medical Physics Department, 
Coordinator for Radiological Protection, Deputy Head of the Department of 
Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical 
University of Silesia in Katowice

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Including superficial white matter in cortical parcellation

[Thomas, George]

External Email - Use Caution

Dear Freesurfer Experts,

I am interested in generating a volumetric segmentation and parcellation of the 
HCP-MMP1 atlas using mri_surf2volseg - and I have previously done this like so:

mri_surf2volseg --o $sub/HCP-MMP1_fsSpace.mgz \
--label-cortex --i $sub/mri/aseg.mgz --threads 4 \
--lh-annot $sub/label/lh.HCP-MMP1.annot 1000 
--lh-cortex-mask $sub/label/lh.cortex.label \
--lh-white $sub/surf/lh.white --lh-pial 
$sub/surf/lh.pial \
--rh-annot $sub/label/rh.HCP-MMP1.annot 2000 
--rh-cortex-mask $sub/label/rh.cortex.label \
--rh-white $sub/surf/rh.white --rh-pial 
$sub/surf/rh.pial


However rather than use the regular white matter surface generated by recon-all 
(as above), I want to parcellate between the pial surface and a superficial 
white matter surface 1mm below the GM/WM boundary.

I have generated this superficial white matter (SWM) surface for both 
hemispheres like so:
mris_expand lh.white -1 lh.SWM.1mm

My first though was just to replace the --rh-white / --lh-white inputs with the 
SWM surface, but after running this, the output remains the same.

I think I may also need use a different input than aseg.mgz, but not sure what 
this would be or how to generate it.

Any assistance you could offer with the would be greatly appreciated.

Many thanks,
George

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

[Zollei, Lilla,Ph.D.]

Hi Amrita,

The download link has been sent to you.

The thalamus does get segmented with infantFS and the LUT is the same as for 
the adult recon. I would process the 11 year old data with the adult pipeline.

Lilla


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

Sent: Monday, January 8, 2024 7:17 PM
To: fsbuild 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Infant fs


External Email - Use Caution

Thanks. I had filled out the form. How long do they take to respond? Also can I 
do subcortical thalamic segmentation with it? How is the LUT calculated both 
for infants and adults? Would you recommend an eleven year old's data analyzed 
by regular FS or infant FS?

On Mon, Jan 8, 2024, 6:19 PM fsbuild 
mailto:fsbu...@contbay.com>> wrote:

Looks like you need to fill out the request form,

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS

- R.

On Jan 8, 2024, at 18:12, Amrita Pal 
mailto:palamritaor...@gmail.com>> wrote:


External Email - Use Caution

Hello

I am trying to use the infant fs for processing my pediatric data. Where can I 
download the package?

Thanks and Regards
Amrita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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.