Hi Ali
Can you send us the full command line and output in general? What directory are
you running that from? If not the surf dir then you need to include paths to
the input and output patches (BTW I wouldn’t name the output “.3D”. Our naming
convention is to use .patch as the extension of all of them, and have .3D.patch
be the input to mris_flatten and .flat.patch be the output)
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Monday, December 6, 2021 10:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
External Email - Use Caution
I've made the patch and saved it and am now trying to flatten using
"mris_flatten lh.full.patch.3D lh.full.flat.patch.3D" but it is giving errors:
error: No such file or directory
error: MRISread(/Users/ali/lh.smoothwm): could not open file
error: No such file or directory
error: mris_flatten: could not read surface file /Users/ali/lh.smoothwm
I can see the lh.full.patch file and smoothwm file in the surf folder.
Thanks
On Mon, 6 Dec 2021 at 15:35, Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
It should be displayed by default, but you can also load it by clicking the
curvature pulldown menu and then “Reload…”
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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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,
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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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
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
Can you send us the full command line and output in text?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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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
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
No, there is no auto-cutting. You need to cut your own patch
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto: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.
thanks, Ali
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