Re: [Freesurfer] Longitudinal Stream Problem

[Douglas N. Greve]

OK, I have it now and am able to verify the problem. It's really strange 
-- I don't know why it is behaving like this. It may take me a few days 
to dig into.


On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:


External Email - Use Caution

Sorry I’m not sure why it didn’t upload.  I just tried it again. 
danielianall.tar.gz  - Should include all parts.  EM2 is the 
cross-sectional.  EM is the base.  EM2.long.EM is the long. I also 
tried sending just the base again. danielianbase.tar.gz.


Thanks,

Laura

*From: *"Douglas N. Greve" 
*Reply-To: *Freesurfer support list 
*Date: *Thursday, June 18, 2020 at 9:12 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it?

On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Hi Douglas,

OK I just uploaded the base separately.  danielianbase.tar.gz  I
thought it was part of the original bundle.  Sorry!

Laura

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Tuesday, June 16, 2020 at 10:10 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

I have your data, but it does not have the base image. Can you
upload that as well?

On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Hi Douglas,

I just upload the files as danielian.tar.gz.  I didn’t notice
any damage or artifact on this particular brain or the others
that had this same problem.  This subject is a healthy control
and most of the subjects (3 of 4) that are having this problem
are healthy.  For each we used 2 T1s for the original
cross-sectional input.  The cross was reconstructed fine as
was the base and the 2 other longitudinal timepoints for this
same subject.  The same is the case with the others I’m having
trouble with – all of the their other timepoints are fine for
the cross/base/longitudinal surfaces.  The warped surfaces are
always lower posterior (cerebellum adjacent) and sometimes
also temporal.  Upper cortical and frontal regions are unaffected.

Thanks for your help!

Laura

*From: *"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Friday, June 12, 2020 at 10:35 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

Hard to tell from just that view. Was there a lot of brain
change with that time point? Or was there an MRI artifact? If
no to both, then you can upload all the cross, the base, and
that one long. Follow instructions below (you can make one
tarball for all subjects)

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subjects.tar.gz ./subject1 ./subject2
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 subjects.tar.gz
Send an email that the file has been and the name of the file.






On 6/9/2020 6:32 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

*External Email - Use Caution *

Hi, I’ve finished processing a data set that included
longitudinal data and I’m having a problem with a small
percentage of the longitudinal timepoints.  To review what
I’ve done, I edited all of the individual
(cross-sectional) timepoints until the wm and pial
surfaces were correct, then created the base and edited
that until it looked good, and then created the
longitudinal files for each cross-sectional timepoint. 
Most of these did not need editing and some needed slight
edits to either wm or brainmask which corrected the
longitudinal surfaces.

However, in a small handful of cases, the wm/pial surfaces
were so distorted that editing would not fix the problem.
In these cases, longitudinal surfaces were very different
from both the original cross-section and base.  I’ve tried
to attach a file that shows an 

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Katsumi, Yuta]

Great, thanks so much again for your input, Matt/Tim/Bruce.

Yuta

On 6/19/20, 1:37 PM, "Glasser, Matthew"  wrote:

External Email - Use Caution

After you convert to GIFTI at fsaverage 164k, you can use these 
instructions to get to fs_LR:

 
https://www.google.com/url?sa=t=j==s=web==2ahUKEwiyj9jetI7qAhWNVs0KHR5gCtEQFjABegQIBBAB=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf=AOvVaw0PXEiAKfGjdiN2DJcF7nuI

Matt.

On 6/19/20, 10:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Fischl, Bruce"  wrote:

* External Email - Caution *

In general almost all of our binaries will read or write almost all 
formats we support. There are some exceptions to this, but it is generally true

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my 
overlay files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the 
command that Tim suggested below does indeed seem to work.

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only 
could be outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the 
full 162k fsaverage mesh, but once you have the full fsaverage version, to 
convert to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" 
 wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  
What fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert 
that to GIFTI in full resolution fsaverage space and from there we can help you 
get it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 

> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer 
overlays in the HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing 
magnitude of functional connectivity at each vertex) that has been computed in 
16k fsaverage space that I want to display on a fs_LR surface. I was wondering 
if there’s a way to convert this file (which is in .mgh extension now) to 
.dscalar so it’d be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of 
"Glasser, Matthew" 
> Reply-To: Freesurfer support list 

> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer 
overlays in the HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 

> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in 
the HCP format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know 

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

After you convert to GIFTI at fsaverage 164k, you can use these instructions to 
get to fs_LR:

 
https://www.google.com/url?sa=t=j==s=web==2ahUKEwiyj9jetI7qAhWNVs0KHR5gCtEQFjABegQIBBAB=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf=AOvVaw0PXEiAKfGjdiN2DJcF7nuI

Matt.

On 6/19/20, 10:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Fischl, Bruce"  wrote:

* External Email - Caution *

In general almost all of our binaries will read or write almost all formats 
we support. There are some exceptions to this, but it is generally true

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my 
overlay files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the 
command that Tim suggested below does indeed seem to work.

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the 
full 162k fsaverage mesh, but once you have the full fsaverage version, to 
convert to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew" 
 wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  
What fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert 
that to GIFTI in full resolution fsaverage space and from there we can help you 
get it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in 
the HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude 
of functional connectivity at each vertex) that has been computed in 16k 
fsaverage space that I want to display on a fs_LR surface. I was wondering if 
there’s a way to convert this file (which is in .mgh extension now) to .dscalar 
so it’d be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of 
"Glasser, Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in 
the HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of 
"Katsumi, Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> The materials in this message are private and may contain 
Protected Healthcare Information or other information of a sensitive nature. If 
you are not 

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Fischl, Bruce]

In general almost all of our binaries will read or write almost all formats we 
support. There are some exceptions to this, but it is generally true

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay 
files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the command 
that Tim suggested below does indeed seem to work. 

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 
162k fsaverage mesh, but once you have the full fsaverage version, to convert 
to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  
wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  What 
fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert that 
to GIFTI in full resolution fsaverage space and from there we can help you get 
it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude of 
functional connectivity at each vertex) that has been computed in 16k fsaverage 
space that I want to display on a fs_LR surface. I was wondering if there’s a 
way to convert this file (which is in .mgh extension now) to .dscalar so it’d 
be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of "Glasser, 
Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> 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.
>
> 
> 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 

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Fischl, Bruce]

mri_surf2surf will do it, but you are probably better off going directly to 
fsaverage rather than downsampling and upsampling

cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tim Schäfer
Sent: Friday, June 19, 2020 9:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k 
fsaverage mesh, but once you have the full fsaverage version, to convert to 
gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  wrote:
> 
> 
> External Email - Use Caution
> 
> The appropriate GIFTI extension for that would be .func.gii.  What fsaverage# 
> space is that?  Hopefully FreeSurfer provides a tool to convert that to GIFTI 
> in full resolution fsaverage space and from there we can help you get it to 
> CIFTI in fs_LR.
> 
> Matt.
> 
> From:  on behalf of "Katsumi, 
> Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
> HCP format
> 
> 
> Hi Matt,
> 
> For instance, I have a statistical map (e.g., showing magnitude of functional 
> connectivity at each vertex) that has been computed in 16k fsaverage space 
> that I want to display on a fs_LR surface. I was wondering if there’s a way 
> to convert this file (which is in .mgh extension now) to .dscalar so it’d be 
> CIFTI/wb compatible.
> 
> Thanks,
> Yuta
> 
> From:  on behalf of "Glasser, 
> Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
> HCP format
> 
> 
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
> 
> Matt.
> 
> From:  on behalf of "Katsumi, 
> Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
> format
> 
> 
> Dear FreeSurfer community,
> 
> I would like to be able to display OVERLAY files generated in FreeSurfer on a 
> surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
> in their documentation 
> (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
>  that any surfaces to be converted to fs_LR need to be in .gii first, but I 
> know mris_convert doesn’t take overlay files as input. It would be great if 
> you could please let me know how I might be able to achieve this task.
> 
> Thanks,
> Yuta
> 
> 
> 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.
> 
> 
> 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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

___
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] Visualization of FreeSurfer overlays in the HCP format

[Katsumi, Yuta]

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay 
files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the command 
that Tim suggested below does indeed seem to work. 

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 
162k fsaverage mesh, but once you have the full fsaverage version, to convert 
to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  
wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  What 
fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert that 
to GIFTI in full resolution fsaverage space and from there we can help you get 
it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude of 
functional connectivity at each vertex) that has been computed in 16k fsaverage 
space that I want to display on a fs_LR surface. I was wondering if there’s a 
way to convert this file (which is in .mgh extension now) to .dscalar so it’d 
be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of "Glasser, 
Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> 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.
>
> 
> 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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and 
Psychotherapy
University Hospital Frankfurt, 

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim 
Schäfer"  
wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k 
fsaverage mesh, but once you have the full fsaverage version, to convert to 
gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  What 
fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert that 
to GIFTI in full resolution fsaverage space and from there we can help you get 
it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude of 
functional connectivity at each vertex) that has been computed in 16k fsaverage 
space that I want to display on a fs_LR surface. I was wondering if there’s a 
way to convert this file (which is in .mgh extension now) to .dscalar so it’d 
be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of "Glasser, 
Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in FreeSurfer 
on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team 
states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> 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.
>
> 
> 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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and 
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Tim Schäfer]

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k 
fsaverage mesh, but once you have the full fsaverage version, to convert to 
gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  wrote:
> 
> 
> External Email - Use Caution
> 
> The appropriate GIFTI extension for that would be .func.gii.  What fsaverage# 
> space is that?  Hopefully FreeSurfer provides a tool to convert that to GIFTI 
> in full resolution fsaverage space and from there we can help you get it to 
> CIFTI in fs_LR.
> 
> Matt.
> 
> From:  on behalf of "Katsumi, Yuta" 
> 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
> format
> 
> 
> Hi Matt,
> 
> For instance, I have a statistical map (e.g., showing magnitude of functional 
> connectivity at each vertex) that has been computed in 16k fsaverage space 
> that I want to display on a fs_LR surface. I was wondering if there’s a way 
> to convert this file (which is in .mgh extension now) to .dscalar so it’d be 
> CIFTI/wb compatible.
> 
> Thanks,
> Yuta
> 
> From:  on behalf of "Glasser, 
> Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
> format
> 
> 
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
> 
> Matt.
> 
> From:  on behalf of "Katsumi, Yuta" 
> 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
> 
> 
> Dear FreeSurfer community,
> 
> I would like to be able to display OVERLAY files generated in FreeSurfer on a 
> surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
> in their documentation 
> (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
>  that any surfaces to be converted to fs_LR need to be in .gii first, but I 
> know mris_convert doesn’t take overlay files as input. It would be great if 
> you could please let me know how I might be able to achieve this task.
> 
> Thanks,
> Yuta
> 
> 
> 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.
> 
> 
> 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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Glasser, Matthew]

External Email - Use Caution

The appropriate GIFTI extension for that would be .func.gii.  What fsaverage# 
space is that?  Hopefully FreeSurfer provides a tool to convert that to GIFTI 
in full resolution fsaverage space and from there we can help you get it to 
CIFTI in fs_LR.

Matt.

From:  on behalf of "Katsumi, Yuta" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 10:43 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


Hi Matt,

For instance, I have a statistical map (e.g., showing magnitude of functional 
connectivity at each vertex) that has been computed in 16k fsaverage space that 
I want to display on a fs_LR surface. I was wondering if there’s a way to 
convert this file (which is in .mgh extension now) to .dscalar so it’d be 
CIFTI/wb compatible.

Thanks,
Yuta

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 10:37 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


External Email - Use Caution
What kind of data does one display in an “OVERLAY” file?

Matt.

From:  on behalf of "Katsumi, Yuta" 

Reply-To: Freesurfer support list 
Date: Thursday, June 18, 2020 at 5:43 PM
To: Freesurfer support list 
Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format


Dear FreeSurfer community,

I would like to be able to display OVERLAY files generated in FreeSurfer on a 
surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.

Thanks,
Yuta


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.


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] Error with "recon-all -make all" following multiple manual editing

[Niels Bergsland]

External Email - Use Caution

Hi all,
Just following up on this as I've run into the exact same problem. Is there
a different recon-all.makefile that should be used for FS 6/6.0.1 ?

Thanks!


On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE <
matthieuvanhou...@gmail.com> wrote:

> External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> Havng done multiple types of manual editing in two subjects, I relaunched
> the recon-all process (Freesurfer 6.0.1) with the flag "-make all".
>
> However, during the process, I goth for both subjects the following error
> message:
>
> *make: ***
> [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz]
> Error 1*
>
>
> *recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024
> -ccseg ERROR: Flag -ccseg unrecognized.*
>
> Following the troubleshooting site (
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0)
> I have over-writed the "recon-all.makefile" file since I use the 6.0.1
> version of Freesurfer.
>
> Thanks for helping.
>
> Best,
>
> Matthieu
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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