Re: [Freesurfer] Hypothalamus segmentation output

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Perfect! Thank you so much for the clarification.

Stay safe

On Tue, Mar 16, 2021 at 11:53 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Alex,
>
> As explained in the wiki, if you run the module on a FreeSurfer processed
> subject, the output will be in the subject’s mri directory, and will be
> called: hypothalamic_subunits_seg.v1.mgz
>
> So you could run something like:
>
> cd $SUBJECTS_DIR//mri
>
> freeview nu.mgz hypothalamic_subunits_seg.v1.mgz
>
>
>
> If you ran the module on a raw t1 scan, then the output will be wherever
> you specified with the flag -o
>
>
>
> Kind regards,
>
>
>
> Eugenio
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://secure-web.cisco.com/1bFVqbSu5YkzvYL_x_m0f_DQcxx0pZQ8vp0u5Bxy2EBQbGbToWGK-wF62O3dsAjQW4L_UiqVdRONNu-gDz2SA65SFAs67GChhvGZbHe39NTU68i1DO0k3FK51fPTaffWcB3IyhBcaD1RzED6clFlJpHU9JHCTSSwfijZZQ1bwS-LmPM3IRNzJbALP55318jrSYPbJ4Tks1VVYQy8REzjYFAs66Db1vN7KXIYAsKn2Q6r9f4qsBVdDTynqgdTOaZtkKVFLGzvpEJyFh7uHTXyHrg/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Lab of
> Autism and Developmental Neuroscience, Lab of Autism and Developmental
> Neuroscience" 
> *Reply-To: *Freesurfer support list 
> *Date: *Tuesday, March 16, 2021 at 23:22
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Hypothalamus segmentation output
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer experts,
>
>
>
> Hope that you all are well and stay safe.
>
>
>
> I would like some help figuring out the code to open the output for the
> hypothalamus segmentation (via freeview). Does anyone have this info? I
> didn't find it on the website.
>
>
>
> Thank you so much!
>
>
>
> All the best,
>
> Alex
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1H38lylt88AJLP0jL_vYdoopjyZHyqCy_wku5EU2mLyZqW5rT5Zj9tXkU5zuHYgeUvkup8DFaC1Go-eavFyTskXU6gJpETLv-YTrnJmMxtc-BmLwkzTo87MUU66dMbMT0kNvcgpg8DGfgw2FUHZHph_QcuWCdgg5nNrXFjx0iHjzUX2mibXJ5jhg3s3oMcvd_7pdQEgjsLn_NKC_WFrakW29b4KwaGnqGdB8g265etNjqheOkpc9bJcuW2QbeQTaQ196RRLyXhZJ5UHNifchvnA/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

Re: [Freesurfer] Hypothalamus segmentation output

[Iglesias Gonzalez, Juan E.]

Dear Alex,
As explained in the wiki, if you run the module on a FreeSurfer processed 
subject, the output will be in the subject’s mri directory, and will be called: 
hypothalamic_subunits_seg.v1.mgz
So you could run something like:
cd $SUBJECTS_DIR//mri
freeview nu.mgz hypothalamic_subunits_seg.v1.mgz

If you ran the module on a raw t1 scan, then the output will be wherever you 
specified with the flag -o

Kind regards,

Eugenio



Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 16, 2021 at 23:22
To: Freesurfer support list 
Subject: [Freesurfer] Hypothalamus segmentation output


External Email - Use Caution
Dear Freesurfer experts,

Hope that you all are well and stay safe.

I would like some help figuring out the code to open the output for the 
hypothalamus segmentation (via freeview). Does anyone have this info? I didn't 
find it on the website.

Thank you so much!

All the best,
Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Hypothalamus segmentation output

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

External Email - Use Caution

Dear Freesurfer experts,

Hope that you all are well and stay safe.

I would like some help figuring out the code to open the output for the
hypothalamus segmentation (via freeview). Does anyone have this info? I
didn't find it on the website.

Thank you so much!

All the best,
Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Meylin overlay

[Glasser, Matthew]

External Email - Use Caution

There is a bug in Freeview, I believe it has been fixed in the dev build.

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Tuesday, March 16, 2021 at 10:38 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Meylin overlay



External Email - Use Caution
Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but worked 
fine with freesurfer 6. With version 7.1 it failed to load the gii file. Any 
idea how to fix it?

Mudathir





On Mar 16, 2021, at 21:08, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

External Email - Use Caution

You should be able to load files like 
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
 in Freeview.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of バキット・ムダシル mailto:m-bak...@fmu.ac.jp>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, March 15, 2021 at 10:18 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Meylin overlay

External Email - Use Caution
Dear freesurfer experts,

Is there a way to import the individual surface myelin maps from the human 
connectome project database to freesurfer and use them as overlays? Or can we 
create them in freesurfer?

Mudathir








The materials in this message are private and may contain Protected Healthcare 
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 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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



The materials in this message are private and may contain Protected Healthcare 
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 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Meylin overlay

[バキット・ムダシル]

External Email - Use Caution

Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but worked 
fine with freesurfer 6. With version 7.1 it failed to load the gii file. Any 
idea how to fix it?

Mudathir





> On Mar 16, 2021, at 21:08, Glasser, Matthew  wrote:
> 
> External Email - Use Caution
> 
> 
> You should be able to load files like 
> ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
>  in Freeview.
> 
> Matt.
>  
> From:  > on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Reply-To: Freesurfer support list  >
> Date: Monday, March 15, 2021 at 10:18 PM
> To: "freesurfer@nmr.mgh.harvard.edu " 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Meylin overlay
>  
> External Email - Use Caution
> Dear freesurfer experts,
>  
> Is there a way to import the individual surface myelin maps from the human 
> connectome project database to freesurfer and use them as overlays? Or can we 
> create them in freesurfer?
>  
> Mudathir
>  
>  
>  
>  
> 
>  
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare 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 strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://secure-web.cisco.com/1dVyyIVOL4vUyrUJnnyD5dKmi7hFYV2vkiJm8YkOpaSoUJtUrZUhJkzn_Vyu4jjgR66BUATSUNxEuPP1slYgmzRF0h2aCbtsHujvj-8_gLa5GbJviT_bDBo82N2AHNv0ECL07qpGfwA1bREYDl8ymRlISm9o0_YSJjENL1fcxNyb1BXkiEZVKlny0h-XAVgTVWWOM0p-gMxWxM_xlvrWoy8GPir3sfx7_3i1n0MIAMn54ma2Hp3lD_ubO1bVltzsRWS0DbE2J0bWGHSg8kr1H4A/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

Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

[Laurel Quinlan]

External Email - Use Caution

Okay, thank you very much!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, March 16, 2021 11:03 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

Then it is probably ok

On 3/8/2021 1:46 PM, Laurel Quinlan wrote:

External Email - Use Caution

The subcortical structures do look okay to me.

-Laurel

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Monday, March 8, 2021 9:48 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

Hard to say from a description. If you look at the subcortical structures, do 
they look like they are accurate?

On 3/1/2021 4:36 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi Freesurfer Team,

I am checking over the aseg on one of my subjects and notice that there are 
large portions of cortex missing anteriorly. The omission does not seem to 
affect any subcortical structures. Do you think that the subcortical values 
extracted from this subject are okay, even if there is cortex missing?

Thanks!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




___
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/10idtRXSHyTwmjyIQerrZT9JruXWx2B6IvTKeOrShRhrGnWWIgPhROB8apwD0j16GtIURfugADBv4dc2fTenzTXbC-9_jAiNhCY1XbxkKXP9zXKjV5jSl7sMu_gK24yqqCBfmWc-O_4jBO5OkQX1LsVgNPi8ap3vuphriNf703NPIe2jslcOzmX99N7jeFshWkvaOI7jCl-S6mWgTdWhwNAhVXZaGCbrYvYxg1oFOMBXkt2HWZJ9XWkNnNrrIk1vwsKEZpuOuchHjxrQNep3KSA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/10idtRXSHyTwmjyIQerrZT9JruXWx2B6IvTKeOrShRhrGnWWIgPhROB8apwD0j16GtIURfugADBv4dc2fTenzTXbC-9_jAiNhCY1XbxkKXP9zXKjV5jSl7sMu_gK24yqqCBfmWc-O_4jBO5OkQX1LsVgNPi8ap3vuphriNf703NPIe2jslcOzmX99N7jeFshWkvaOI7jCl-S6mWgTdWhwNAhVXZaGCbrYvYxg1oFOMBXkt2HWZJ9XWkNnNrrIk1vwsKEZpuOuchHjxrQNep3KSA/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

Re: [Freesurfer] Matlab Runtime error line 334

[Hoopes, Andrew]

Hi Matt,

Hopefully this isn’t specific to M1, but I’m not sure it would be in this case. 
Maybe try running fs_install_mcr with sudo in front? Some users are suggesting 
it here:
https://www.mathworks.com/matlabcentral/answers/176228-error-message-install_unix-not-found

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cleary, Matthew 

Date: Friday, March 12, 2021 at 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Matlab Runtime error line 334
External Email - Use Caution

Hi team,

I’m wondering if I could please ask for help - I am trying to install 
fs_install_mcr R2014b on a 2020 M1 chip MacBook. I’m encountering an error at 
the end, that goes as follows;

inflating: sys/java/jre/maci64/jre/THIRDPARTYLICENSEREADME.txt
  inflating: sys/java/jre/maci64/jre/Welcome.html
  inflating: trademarks.txt
./install: line 334: 
/var/folders/2f/fyngt3b52mn39mcc6_419q8hgn/T/tmp.rt0pgVdq/bin/unknown/install_unix:
 No such file or directory
ls: 
/var/folders/2f/fyngt3b52mn39mcc6_419q8hgn/T/tmp.rt0pgVdq/install-target/v*:
 No such file or directory

Do you have any idea how I can fix this? Any help would be massively 
appreciated.

Kindest regards,
Matt

___
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

Re: [Freesurfer] freesurfer install error

[fsbuild]

External Email - Use Caution

It reads like you are trying to install on an Ubuntu system, e.g., Ubuntu 18 or 
Ubuntu 20? On Ubuntu you can try the install command,$ sudo apt 
installlibjpeg62

Also it would be good to know what freesurfer release you are installing, e.g., 
7.1.1.
Something may not be right with your environment for remote X programs. I 
would check you have the DISPLAY environment variable setup in your xshell or 
xmanager setup. On my terminal DISPLAY is set to,
$ echo $DISPLAY:0
I don’t know how xshell and xmanager setup your X environment, but I would 
first try running a simple X windows program like xeyes and get that to work 
(displays a pair of eyes that track the cursor) before running tksurfer, etc.
- R.

On Mar 16, 2021, at 07:17, 1248742467 1248742...@qq.com 
wrote:External Email - Use 
CautionHello, FsAfter 
installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all -- help 
to verify whether the installation is successful.The first and fourth 
commands are OK, but the second and third commands display the same error: 
glut: fatal error in tksurfer.bin : could not open display: 
localhost:17.0.I use xshell as a terminal, and I have installed xmanager. I 
used to be able to use it, but now I have problems.And when I use the Freeview 
command, an error is reported as follows: freeview.bin : error while loading 
shared libraries: libjpeg.so .62: cannot open shared object file: No such 
file or directoryDo you know how to solve the above problems?Looking forward to 
your reply___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

Re: [Freesurfer] Putamen and claustrum

[Douglas N. Greve]

Hi Donatas, did I write that? I don't remember how it works. I think it 
is just some minor mechanical clean up.

doug


On 3/16/2021 12:37 PM, Donatas Sederevicius wrote:


External Email - Use Caution

Dear FreeSurfers,
I had a look at the RB_all_2020-01-02.gca atlas and there was no 
probabilistic information regarding the claustrum. However, in the 
mailing archive I have found the following:

"On 2 May 2017, at 17:57, Douglas Grevewrote:
[…] Putamen should be smaller because we now try to remove claustrum."

Could you give a brief description of how you try to achieve it (if it 
is still the case)?


Thank you.
-Donatas

___
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

Re: [Freesurfer] Help

[Douglas N. Greve]

We don't have a lobar segmentation. You can get whole cerebellum (GM and 
WM) from our standard analysis (recon-all) or using samseg.

On 3/5/2021 3:27 PM, Murray Howerth wrote:
>  External Email - Use Caution
>
> I am new to this platform and would like some direction as how to obtain 
> adjusted cerebellar volumes, specifically lobular cerebellum structure.
> With thanks,
> M
>
> ___
> 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

[Freesurfer] Putamen and claustrum

[Donatas Sederevicius]

External Email - Use Caution

Dear FreeSurfers,


I had a look at the RB_all_2020-01-02.gca atlas and there was no probabilistic 
information regarding the claustrum. However, in the mailing archive I have 
found the following:

"On 2 May 2017, at 17:57, Douglas Greve wrote:

[…] Putamen should be smaller because we now try to remove claustrum."

Could you give a brief description of how you try to achieve it (if it is still 
the case)?

Thank you.
-Donatas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

What command are you using? make_average_subject? Send the command line 
and terminal output


On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from a set of subjects, but 
keep getting an error that says "mghRead(mri/norm.mgz, -1): could not 
open file". I've read that several others have solved this issue by 
installing the patch available at *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ 
. 
I did this, but continue to get the same error. I'm working with 
Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've 
attached the recon-all.log below, but please let me know if you need 
additional information.


Any insight on this would be appreciated! Thank you!

Jordan

--
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://ucrkindlab.com 




___
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

Re: [Freesurfer] Flip image (resize)

[Douglas N. Greve]

You should contact SPM

On 3/10/2021 11:57 AM, Ramesh Babu wrote:


External Email - Use Caution

Dear Experts,

The fMRI data, when viewed in SPM, some images have 3x3x4 voxel 
dimensions and some images have -3x3x4. Should I flip the image (using 
resize option) so that all images will have the same dimensions? or 
Should I leave it without flipping?


Please give your suggestions.

Regards
Ramesh

___
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

Re: [Freesurfer] Absolute volume difference between Freesurfer 6.0 and 7.1

[Douglas N. Greve]

I'm not sure where the differences are coming from, but it sounds like 
the range we are seeing. My guess is that the intensity normalization 
changes are the cause. There are always voxels on the edge of a 
structure that are ambiguous, and a slight change in intensity can cause 
their segmentation to switch.


On 3/10/2021 10:11 AM, Lee, Sang Hoon wrote:


External Email - Use Caution

External Email - Use Caution

I recently installed version 7.1, and I compared absolute volumes with 
version 6.0, and I realized that there are some significant 
differences in some brain structures (e.g. Hippocampus and amygdala).  
In some cases, the differences are more than 7%-14%.
I understand that I should not be mixing the version when I process my 
datasets, but can you let me know what the main reason for the 
differences is, and how much should I expect?


thank you.
Sang

___
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

Re: [Freesurfer] editing surfaces in two different Freesurfer versions

[Douglas N. Greve]

Yes, you should be able to run 7.1 recon-all on 5.3/6.0 and it should 
respect the edits (but make a copy before you do!)

On 3/9/2021 6:59 PM, Lara Foland-Ross wrote:
>  External Email - Use Caution
>
> Hi there,
>
> We are making the switch to Freesurfer v7.1 and wondering - can we continue 
> editing surfaces in 7.1 that had previously undergone editing in versions 5.3 
> or 6.0?
>
> Thanks,
> Lara
>
> Lara Foland-Ross, Ph.D.
> Senior Research Associate and Imaging Lab Manager
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
>
> ___
> 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

Re: [Freesurfer] Troubleshooting: Soft Failures

[Douglas N. Greve]

Can you send the recon-all log file?

On 3/9/2021 2:06 AM, 崔鹏程 wrote:


External Email - Use Caution

Hi FreeSurfer experts,

Recently, I used Fresurfer's */recon-all/*toprocess our own T1 
MRIbrain volumes which is 0.7 m3 isotropic.For most young brain cases, 
FS performs very well, the segmention is great.But for almost every 
elderly brain case, the segmention is inaccurate visibly.The figure is 
the same slice of T1 data and aseg.mgz , */the GM is mislabeled as 
wm-hypointensities/* .


I found some solutions to this problem.But these solutions all require 
manual editing, which will take a long time.Is there a way to 
automatically solve this problem by setting some parameters?


Thank you for your attention and your help!

Cui


___
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

Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?

[Douglas N. Greve]

Then it is probably ok

On 3/8/2021 1:46 PM, Laurel Quinlan wrote:


External Email - Use Caution

The subcortical structures do look okay to me.

-Laurel

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, March 8, 2021 9:48 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Aseg missing frontal portions - 
subcortical okay?
Hard to say from a description. If you look at the subcortical 
structures, do they look like they are accurate?


On 3/1/2021 4:36 PM, Laurel Quinlan wrote:


External Email - Use Caution

Hi Freesurfer Team,

I am checking over the aseg on one of my subjects and notice that 
there are large portions of cortex missing anteriorly. The omission 
does not seem to affect any subcortical structures. Do you think that 
the subcortical values extracted from this subject are okay, even if 
there is cortex missing?


Thanks!

*Laurel Quinlan*
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison


___
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


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

Re: [Freesurfer] Failed tissue type check {Disarmed}

[Douglas N. Greve]

I don't know. Can you upload the data so I can take a look? Instructions 
are below. I'd need both the anatomical data (output of recon-all) and 
input.nii.gz and PET.lta


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 3/8/2021 11:47 AM, Julie Ottoy wrote:


External Email - Use Caution

Hi Doug,

Any other suggestions I could try? It seems to be only an issue with 
the non-pvc data.


Thanks
Julie

On Tue, 2 Feb 2021 at 11:10, Julie Ottoy > wrote:


Hi Doug,

I tried these fixes but they still give me the error message
below. I did replace it in the gtmseg.ctab though -- should it be
perhaps the seg.ctab in the aux folder ?

Thanks,
Julie

On Tue, 12 Jan 2021 at 10:37, Julie Ottoy
mailto:julie.jj.ot...@gmail.com>> wrote:

Hi Doug

I tried that as well but getting the same error as with
--replace 29 3.


ERROR: CTABpruneCTab(): ctab does not have segid 2



Thanks,
julie

On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:

Try using --replace 29 2


On 12/29/2020 12:48 PM, Julie Ottoy wrote:


External Email - Use Caution

Hi Doug

Thanks for your reply. I tried both your suggestions, but
it seems as though they both ran into an error.

For your first suggestion, i.e. adding --replace 29 3 to
the command line of gtmpvc, I get the error:

Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz

Loading seg ctab 057_S_5295re/mri/gtmseg.ctab

Reading 057_S_5295re/mri/gtmseg.lta

Replacing 19

Pruning ctab

ERROR: CTABpruneCTab(): ctab does not have segid 3


For your second suggestion, i.e. I replaced the following
line in the ctab:

  29  Left-undetermined 135 206 235    0  -1

==> replaced by:  29  Left-undetermined               135
206 235    0  3


I get the error:

Computing Seg in input space

Building GTM DoVoxFracCor=0

ERROR: creating region for nthseg=12, segid=29,
Left-undetermined

It may be that there are no voxels for this seg when
mapped into the input space.

Check
057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz
and the registration

Build time 5.9690, err = 1


Thank you,

Julie


On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>
wrote:

You can use the fix from my previous email or you can
add the following line any were into the gtmseg.ctab
file:
 29 Left-undetermined 135 206 235 0 3


On 12/18/2020 11:06 PM, Julie Ottoy wrote:


External Email - Use Caution

Sorry I would like to correct my previous post. The
subject also failed with PVC.
I see now that the issue is happening during the gtm
seg stage where it gives the error: WARNING: segid  
29 Left-undetermined tissue type is not set.
For your information: I ran the standard FS and
petsurfer pipeline as outlined on the wiki. I tried
two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm
--subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo
--subsegwm --subseg-cblum-wm

Thank you for your help,
Julie

On Fri, 18 Dec 2020 at 00:09, Julie Ottoy
mailto:julie.jj.ot...@gmail.com>> wrote:

External Email - Use Caution


  Dear Doug,


I have the same issue as the people below. I was
wondering if this was solved in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe
flags to not do PVC and got the following error
in only one of my subjects. When I ran the same
subject with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf

Re: [Freesurfer] Problem with freesurfer measures

[Douglas N. Greve]

I think they will give very similar results, but my guess is that #1 is 
a little better


On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

I want to use the annotation file created by myself in fsaverage to 
calculate the anatomical stats, but i dont know what is the best 
workflow.


1. Convert the annotation file to each subject space using 
mri_sur2surf and using mri_anatomical_stats in each subject
2. Convert the surface of each subject to fsaverage space and use 
mri_segstats to obtain the data, in this case i dont know what surface 
i have to convert to fsaverage space to do it (i can see thickness 
(lh/rh.thickness) and volume (lh/rh.volume) but not folding index and 
white matter volume)


Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce 
(mailto:bfis...@mgh.harvard.edu>>) escribió:


Hi Alberto

 1. And 4. Are not properties of single surfaces – they are
computed from the white and the pial. For 2 and 3 that is
really up to you

Cheers
Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Problem with freesurfer measures

*External Email - Use Caution *

Hello Freesurfer team, I am using an annotation file that i've
created previously to obtain the measures of some ROIs. To do that
i am using de commands mri_surf2surf and mri_segstats. I want to
obtain the following measures:

1. Gray and White Matter Volume

2. Folding Index

3. Curvature measures

4. Thickness

However I don't know what surface in the surf folder of each
subject I have to use. Could u help me?

___
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


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

Re: [Freesurfer] Cortical surface analysis

[Douglas N. Greve]

On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:


External Email - Use Caution

Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone can help me.

My goal is to be able to visualise electrodes contacts that are on 
lying on the cortical surface on a flat map and a spherical map.


I've run recon-all and created the flatmap.

I'm using Matlab to achieve this and I've loaded the information with 
the lines


lhsphere = 
fs_read_surf('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.sphere');


lhflatpatch=fs_read_patch('/Applications/freesurfer/7.1.1/subjects/IM-0001/surf/lh.full.flat.patch.3D'); 



1. I want to be able to access the coordinates and show the electrons 
on the flat map/ sphere and I was wondering how to do this?  I 
understand that the vertex ID number is what relates the coordinates 
in the original image to these surfaces.  I am wondering how to access 
the vertex ID numbers ?  At the moment I think that I only have access 
to the vertex coordinates and the vertex faces.
The easiest way to do this is probably to map the white or pial xyz into 
an mgz file using mri_surf2surf, eg
mri_surf2surf  --hemi lh   --sval-xyz white --tval lh.white.xyz.mgz   
--s yoursubject

You can then get the xyz of a given vertex by reading
whitexyz = MRIread('lh.white.xyz.mgz');



2. Additionally, I was wondering if there is a way to display the 
surface images through Matlab?  What would be the best way to show the 
surface with the electrons overlaid on it?

I know there are ways, but I don't know their details


The version of Freesurfer and the platform that I'm using is outlined 
below:

1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: macOS High Sierra 10.13.6 (17G7024)

I really appreciate any help with this as I'm really stuck.

Thanks in advance for any help.

Kind Regards,
Ornaith O'Reilly

___
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

Re: [Freesurfer] Using Aseg atlas/subcortical segmentation with T2 MRI

[Douglas N. Greve]

There are several things you can try. First, you can use samseg instead 
of recon-all to generate the subcortical segmentation. Samseg works on 
any modality or combination of modalities. Second, you can try to build 
and apply your own atlas. This is more difficult, but you would start 
with gcatrain.





On 3/4/2021 10:26 PM, Choi, Nuri wrote:


External Email - Use Caution

External Email - Use Caution

Hi,

I was wondering if it is possible for me to use FreeSurfer's 
subcortical segmentation feature with T2-weighted images. Our lab was 
hoping to make our own T2-weighted Aseg atlas (which I believe is 
possible with FreeSurfer) and run the subcortical segmentation using 
that atlas. However, since FreeSurfer is designed for T1-weighted 
images, I wasn't sure if it be possible to pass a T2w MRI image 
instead. We don't need any of the other features available from 
FreeSurfer, just the subcortical segmentation. Would doing this step 
for T2 MRI be feasible using FreeSurfer?


Thanks,
-Nuri

_

Nu Ri Choi

Undergraduate Student, Washington University in St. Louis

Computer Science + Math

Mobile: 314-327-2303



___
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

Re: [Freesurfer] mri_surf2surf command error

[Douglas N. Greve]

Can you give the command line that is failing and the terminal output?


On 3/4/2021 12:53 AM, 1248742467 wrote:


?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution

Hello, Fs
I want to template some subject to fsaverage5, but now I meet some 
problems

FreeSurfer version: Fs6
Download the files: HLN-12-2.tar.gz OASIS-TRT-20-1.tar.gz 
?0?2Twins-2-1.tar.gz?0?2?0?2Twins-2-2.tar.gz(https://osf.io/wzqmg/)


Register the following 5 files into the fsaverage5 space:
lh.area?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 lh.jacobian_white?0?2 ?0?2 ?0?2lh.volume ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
?0?2lh.labels.DKT31.manual.annot


The error message:
HLN-12-2: lh.area?0?2 ?0?2 lh.volume?0?2 ?0?2 lh.jacobian_white
?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2can't match the surface 
??148208,146833??
OASIS-20-1?? lh.labels.DKT31.manual.annot
?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2here is a problem with the registration of the 
.annot file?? can't allocate memory

Twins-2-1/Twins-2-2:
?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2File missing: 
lh.area lh.volume lh.jacobian_white

template to fsaverage5 space command: mri_surf2surf
example 1:?0?2 ?0?2mri_surf2surf --srcsubject Afterthought-1 --sval 
thickness --src_type curv --trgsubject fsaverage5 --trgsurfval 
/home/tj/application/freesurfer/subjects/Afterthought-1-target/thickness 
--trg_type curv --hemi rh


example?0?2 2:?0?2 mri_surf2surf --srcsubject OASIS-TRT-20-1 --trgsubject 
fsaverage5 --hemi lh --sval-annot 
/home/tj/application/freesurfer/subjects/OASIS-TRT-20-1/label/lh.labels.DKT31.manual.annot 
--tval 
/home/tj/application/freesurfer/subjects/min_template/OASIS-TRT-20-1-target/lh.labels.DKT31.manual.annot


Do you know how to solve these problem? Could you please download the 
four folder, and template the four file to fsaverage5 space? Then send 
the peocessed file to me.?0?2 Thank you very much!



*??QQ??*

Description.txt 
(1.2K, 
2021??03??04?? 10:52 )
 
??http://mail.qq.com/cgi-bin/ftnExs_download?t=exs_ftn_download=2265303515cb9e9925295e7f103053495506090c075250034b550006011d550407531d545452024b5e57030600555453005d0857363f6122031653475f40150f090b1e414e44615b=fe0560af


HLN-12-2.tar.gz 

Re: [Freesurfer] Two questions about FDR correction

[Douglas N. Greve]

On 3/3/2021 3:45 PM, Funk, Quentin wrote:


External Email - Use Caution

Freesurfer experts,

I have two questions that probably show my lack of understanding of 
many things related to thickness comparisons.


I have a group of controls and a single subject with pathology. I'd 
like to run a thickness analysis comparing them. I realize this is not 
ideal from a statistical standpoint, but due to the rarity of the 
disease, we'd like to see the results anyways.


Currently I'm using mri_glmfit followed by mri_fdr to do this comparison.

My questions are:

1) Is this FDR tool robust enough to handle this type of one-vs-many 
analysis? Is there a better way?

I don't know why it would not be.


2) Generally, for one-vs-many analyses, I'd like to use a z-score. Is 
there a good way to convert this -log10(p) value from sig.mgh into a 
threshold for z.mgh instead? The dumb thing of back converting from 
p-value to z-score doesn't give the same maps once thresholded (there 
is probably an obvious reason for this that I'm missing).

You can take the controls and compute the mean and stddev with
mri_concat controls.stack.mgz --mean --o mean.mgz
mri_concat controls.stack.mgz --std --o std.mgz
Then compute the z for your one subject with
fscalc onesubject.mgz sub mean.mgz div std.mgz -o z.mgz




thank you for any help you can provide!

quentin funk

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 
hospital in Texas for patient care and safety and one of the top 20 
hospitals in the nation. In addition, we are nationally ranked in 11 
specialties, the most in the state, and have been national leaders 
throughout the COVID-19 pandemic in research, offering innovative 
treatments and surpassing CDC safety standards. For more than 100 
years, Houston Methodist has provided the best — and safest — clinical 
care, advanced technology and patient experience. That is our promise 
of leading medicine.



*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* houstonmethodist.org 

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* twitter.com/MethodistHosp 
 

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* facebook.com/HoustonMethodist 



***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
Methodist and/or its relevant affiliates and may contain restricted 
and privileged material for the sole use of the intended recipient(s). 
Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to 
receive for the recipient), please contact the sender and delete all 
copies of the message. Thank you.



___
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

Re: [Freesurfer] Recon-all Ending Fast

[Fischl, Bruce]

Hi Akila

You haven't told it to do anything, so all it does is create the directory 
structure and import the data. You need to add a directive like "- all" to the 
recon-all command line

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of A.R. Sekar
Sent: Tuesday, March 16, 2021 8:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all Ending Fast


External Email - Use Caution

External Email - Use Caution
Hello,

I am trying to run the recon-all function and the whole process is completing 
within a minute or so. I was told that the whole process would take between 
6-24 hours. This is the output I am getting after entering the command:

Akilas-MacBook-Air:Sub01 akilasekar$ recon-all -s sub_01 -i sub1.fspgr.nii

Subject Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

Current Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

INFO: SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects

Actual FREESURFER_HOME /Applications/freesurfer/7.1.1

Darwin Akilas-MacBook-Air.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/7.1.1/subjects/sub_01

\n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz \n

mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz

reading from /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0, -1, 0)

j_ras = (0, 0, 1)

k_ras = (1, 0, 0)

writing to /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz...

/Applications/freesurfer/7.1.1/subjects/sub_01/mri/transforms 
/Applications/freesurfer/7.1.1/subjects/sub_01

/Applications/freesurfer/7.1.1/subjects/sub_01



Started at Tue Mar 16 14:41:43 EAT 2021

Ended   at Tue Mar 16 14:41:49 EAT 2021

#@#%# recon-all-run-time-hours 0.002

recon-all -s sub_01 finished without error at Tue Mar 16 14:41:49 EAT 2021

done

It would great if you can help me out! Thank you!

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

Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Thanks, Franziska.
It seems to be a problem with partial voluming. Cerebral white matter (white 
pixels) mixes with a thin layer of cerebrospinal fluid (black pixels) and the 
result is a bunch of gray pixels that look like the pulvinar. 
Partial voluming is one of the biggest problems with these Bayesian 
segmentation methods, the price you pay for the (huge!) advantage of being 
agnostic to / robust against changes in MR contrast of the input scan...
Unfortunately, there is no easy fix for this at the moment. Normally, the 
increment in volume due to the leak is not as large as it may seem because 
segmentations are weighted by their probabilities when computing volumes.
In the future, we plan to tackle this with deep learning methods that do a 
fantastic job with partial voluming. The problems with this approach are: 1. 
Robustness against contrast changes, and (mostly) 2. Training with ex vivo data 
is tricky.
Cheers,
/Eugenio

 
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 
 
 

On 3/16/21, 03:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

External Email - Use Caution

Dear Eugenio,

here are the zipped norm.mgz and automated segmentations for two subjects:

https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo

Hope this helps!

Best regards,
Franziska


___
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

Re: [Freesurfer] license file not working

[Hoopes, Andrew]

Hi Philipp,

Okay interesting. So it's failing on centos 8. Do you mind sending the license 
file directly to my email (off-list)?

thanks
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Sent: Monday, March 15, 2021 3:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] license file not working

External Email - Use Caution

Hi Andrew,


it works on the "frontend" of  our cluster:


NAME="Scientific Linux"
VERSION="7.9 (Nitrogen)"
ID="scientific"
ID_LIKE="rhel centos fedora"
VERSION_ID="7.9"
PRETTY_NAME="Scientific Linux 7.9 (Nitrogen)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:scientificlinux:scientificlinux:7.9:GA"
HOME_URL="http://www.scientificlinux.org//;
BUG_REPORT_URL="mailto:scientific-linux-de...@listserv.fnal.gov;
REDHAT_BUGZILLA_PRODUCT="Scientific Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT="Scientific Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.9"



But not any more on the nodes:

NAME="CentOS Linux"

VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/;
BUG_REPORT_URL="https://bugs.centos.org/;
CENTOS_MANTISBT_PROJECT="CentOS-8"
CENTOS_MANTISBT_PROJECT_VERSION="8"



Thanks in advance,

best,

Philipp




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Hoopes, Andrew 

Gesendet: Montag, 15. März 2021 20:29
An: Freesurfer support list
Betreff: Re: [Freesurfer] license file not working


Hi Philipp,



Can you let us know the OS and version you’re running on? The license format 
was updated for v6. It should be backwards compatible, but it’s possible it’s 
not anymore on newer systems.



thanks

Andrew



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Date: Monday, March 15, 2021 at 2:36 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] license file not working

External Email - Use Caution

Hi FreeSurfer specalists,



for some historical reconstruction I had to download an old FS5.3-Version,

on a Linux System, untarred etc. - it seems there was no .license = hidden 
license

file coming with the download, and no license.txt file.



I requested one (usual link) and received a license.txt file, and put that

into the FS home folder. When using the command mri_convert I get the

error message that an invalid License file is used.

Questions:



(1) Is a .license file (so, a hidden file) needed for itself or in addition?

(2) Why does a freshly delivered license.txt file not work?

(3) Any other solutions or ideas?



Bw,

Philipp

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

Re: [Freesurfer] Meylin overlay

[Glasser, Matthew]

External Email - Use Caution

You should be able to load files like 
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
 in Freeview.

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Monday, March 15, 2021 at 10:18 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Meylin overlay



External Email - Use Caution
Dear freesurfer experts,

Is there a way to import the individual surface myelin maps from the human 
connectome project database to freesurfer and use them as overlays? Or can we 
create them in freesurfer?

Mudathir







The materials in this message are private and may contain Protected Healthcare 
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 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Recon-all Ending Fast

[A.R. Sekar]

External Email - Use Caution

Hello,

I am trying to run the recon-all function and the whole process is completing 
within a minute or so. I was told that the whole process would take between 
6-24 hours. This is the output I am getting after entering the command:

Akilas-MacBook-Air:Sub01 akilasekar$ recon-all -s sub_01 -i sub1.fspgr.nii

Subject Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

Current Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

INFO: SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects

Actual FREESURFER_HOME /Applications/freesurfer/7.1.1

Darwin Akilas-MacBook-Air.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/7.1.1/subjects/sub_01

\n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz \n

mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz

reading from /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0, -1, 0)

j_ras = (0, 0, 1)

k_ras = (1, 0, 0)

writing to /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz...

/Applications/freesurfer/7.1.1/subjects/sub_01/mri/transforms 
/Applications/freesurfer/7.1.1/subjects/sub_01

/Applications/freesurfer/7.1.1/subjects/sub_01



Started at Tue Mar 16 14:41:43 EAT 2021

Ended   at Tue Mar 16 14:41:49 EAT 2021

#@#%# recon-all-run-time-hours 0.002

recon-all -s sub_01 finished without error at Tue Mar 16 14:41:49 EAT 2021

done

It would great if you can help me out! Thank you!

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

[Freesurfer] freesurfer install error

[1248742467]

External Email - Use Caution

Hello, Fs
After installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all 
-- help to verify whether the installation is successful.
The first and fourth commands are OK, but the second and third commands display 
the same error: glut: fatal error in tksurfer.bin : could not open 
display: localhost:17.0.
I use xshell as a terminal, and I have installed xmanager. I used to be able to 
use it, but now I have problems.
And when I use the Freeview command, an error is reported as follows: 
freeview.bin : error while loading shared libraries: libjpeg.so .62: 
cannot open shared object file: No such file or directory
Do you know how to solve the above problems?




Looking forward to your reply___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

here are the zipped norm.mgz and automated segmentations for two subjects:
https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo

Hope this helps!

Best regards,
Franziska


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