It should be displayed by default, but you can also load it by clicking the curvature pulldown menu and then “Reload…”
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 10:30 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution Thank you that opened up freeview. When I click file to load the curvature file there ain't an option for it. I need the curvature file to guide the cuts or else it will be an estimation. Any ideas why this would be?
Thanks
On Mon 6 Dec 2021, 15:24 Fischl, Bruce, <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: No, it should be:
freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated
the $ means to dereference a variable, so it was trying to find an environment var named IM
cheers Bruce From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 7:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution IM-0001 is the subject name. should i instead be doing freeview -f $SUBJECTS_DIR/$subjects/IM-0001 ?
On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated
output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed
On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali
Can you send us the full command line and output in text?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution Hi Bruce,
I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.
Thanks, Ali
On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali
Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution Hi Bruce,
I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?
Thanks, Ali
On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali
No, there is no auto-cutting. You need to cut your own patch Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution hi all,
I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran
mris_flatten lh.full.patch.3D lh.full.flat.patch.3D
it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.
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