Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

And how does the parcellation look on the surface?

On 3/7/2024 9:53 AM, Hyunchul Lee wrote:


External Email - Use Caution

Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
 wrote:


Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use
with MNE-python for source estimation of SEEG data. My work
relies on having correct labeling of segmentation data. For most
cases, there has been no trouble but I am having trouble where
the cortical parcellation shows up as dots in one hemisphere.
Please see image attached. I also noticed that the lh.ribbon.mgz
is also 'dotty' (also attached). There is no issue with the right
hemisphere. This reconstruction was not manually edited, but only
recon-all was used.

I have tried using mris_volmask --label_left_ribbon, setting the
argument to various values. That didn't work that great -
reducing to 0 basically whites everything out except for the
white matter on the ipsilateral hemisphere and anything 1 or more
produces the same 'dots'. Interestingly the pial and wm surfaces
all look ok. Also, I am not sure if creating the correct
ribbon.mgz is going to fix the aparc.a2009+aseg file.

I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

Hi Brian,

Since there is no output, I’m wondering if it passed reading lh.cortex.label.

Some questions:
1. how did you generate lh.cortex.label? It needs to have the format described 
here - https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles
2. what is your SUBJECTS_DIR?  ‘echo $SUBJECTS_DIR’ will show it.
3. can you try adding ‘-seed 1234’ option to your command line?
 Make sure to add it after ‘-l ’. I just wanted to 
confirm if mris_ca_label read your lh.cortex.label correctly. It should print 
‘setting seed for random number generator to 1234’ if lh.cortex.label is read 
fine.
4. I noticed that you have ‘sub-004’ in the path to lh.cortex.label, but the 
subject id passed to mris_ca_label is ‘001’.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 5:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory


External Email - Use Caution
Thanks again Yujing.

There is not, here is a screen shot of the command (I removed the other inputs 
for clarity) followed by the output, which is just "segmentation fault (core 
dumped)"

[cid:image001.png@01DA7077.5F9EC230]

I think before you asked which free surfer version, which is here:

[cid:image002.png@01DA7077.5F9EC230]

On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
It is hard to tell without the data. Is there any output before the core dump?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Sennott, Liam Ricker
Sent: Wednesday, March 6, 2024 4:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

Sending on behalf of Brian who was having trouble sending a reply:


Dear Yujing,

Thank you! Haha yes, a silly error there with the -1/-l.

When I correctly put -l, I now get the following error: "segmentation fault 
core dumped". Might this error make any sense to you?

Brian


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 11:05 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
Sorry, just recognized it. The option to pass label file is ‘-l’.  It looks 
like you have ‘-1’ instead.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory

I’m not sure which version of Freesurfer you are using. But it seems the 
command line options are not in the right order.  Here is the wiki help - 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ascii: bad interpreter: No such file or directory


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Hello everyone,

I am new to freesurfer so I apologize if this is a simple answer.

i'm running mris_ca_label to get the BN atlas parcellation:

mris_ca_label -1
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label
 001 lh
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot

But it seems freesurfer is having an issue reading my lh.cortex.label file:
/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label:
 ascii: bad interpreter: No such file or directory

Might 

Re: [Freesurfer] Cortical parcellation showing dots

[Hyunchul Lee]

External Email - Use Caution

Yes, it looks fine to me
Those dots seem to lie on the pial surface

On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve 
wrote:

> Have you looked at the actual surface?
>
> On 3/7/2024 2:29 AM, Hyunchul Lee wrote:
>
> External Email - Use Caution
> Hello,
> I'm using Freesurfer recon-all to create reconstructions to use with
> MNE-python for source estimation of SEEG data. My work relies on having
> correct labeling of segmentation data. For most cases, there has been no
> trouble but I am having trouble where the cortical parcellation shows up as
> dots in one hemisphere. Please see image attached. I also noticed that the
> lh.ribbon.mgz is also 'dotty' (also attached). There is no issue with the
> right hemisphere. This reconstruction was not manually edited, but only
> recon-all was used.
>
> I have tried using mris_volmask --label_left_ribbon, setting the argument
> to various values. That didn't work that great - reducing to 0 basically
> whites everything out except for the white matter on the ipsilateral
> hemisphere and anything 1 or more produces the same 'dots'. Interestingly
> the pial and wm surfaces all look ok. Also, I am not sure if creating the
> correct ribbon.mgz is going to fix the aparc.a2009+aseg file.
>
> I would really appreciate your advice.
>
> Best regards,
>
> *Hyunchul Lee*  MBBS PhD
>
> ___
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Re: [Freesurfer] Cortical parcellation showing dots

[Douglas N. Greve]

Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:


External Email - Use Caution

Hello,
I'm using Freesurfer recon-all to create reconstructions to use with 
MNE-python for source estimation of SEEG data. My work relies on 
having correct labeling of segmentation data. For most cases, there 
has been no trouble but I am having trouble where the cortical 
parcellation shows up as dots in one hemisphere. Please see image 
attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also 
attached). There is no issue with the right hemisphere. This 
reconstruction was not manually edited, but only recon-all was used.


I have tried using mris_volmask --label_left_ribbon, setting the 
argument to various values. That didn't work that great - reducing to 
0 basically whites everything out except for the white matter on the 
ipsilateral hemisphere and anything 1 or more produces the same 
'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am 
not sure if creating the correct ribbon.mgz is going to fix the 
aparc.a2009+aseg file.


I would really appreciate your advice.

Best regards,
*
*
*Hyunchul Lee*  MBBS PhD

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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Douglas N. Greve]

Yujing, you can just send Taylor a binary that can be put in the local 
version of $FREESURFER/bin


On 3/6/2024 11:45 AM, Huang, Yujing wrote:


Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit 
SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of 
MRI_CURV_FILE.


We will have a fix in dev version. But I’m not sure how to get around 
this in FS 7.2.


Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Wednesday, March 6, 2024 9:47 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I 
have attached rh.white and rh.area for your review.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Wednesday, March 6, 2024 at 8:37 AM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


It doesn’t look like rh.area is recognized correctly. ‘mri_info 
rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 
dimensions.


I’m not sure where exactly the area values are calculated. What happen 
if you re-run this step?


mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 7:24 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: 
mris_calc could not establish read access to rh.area


*External Email - Use Caution *

Hello Yujing,

Thank you for your quick response!

When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial


I get the following error:

error: No such file or directory

error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): 
could not open file


error: No such file or directory

error:

mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area

        type: unknown

  dimensions: 831 x 10015 x 25953

voxel sizes: -0.00, -0.00,    nan

        type: SHORT (4)

        fov: 1016.473

        dof: 1

      xstart: 0.0, xend: 990983162970892849632569550308376576.0

      ystart: -0.0, yend: 3079152361728581627851833344.0

      zstart: -0.0, zend: -3815443229699337177012458129513775104.0

          TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees


    nframes: 1

    PhEncDir: UNKNOWN

    FieldStrength: 0.00

ras xform present

  xform info: x_r =  -1., y_r =   0., z_r = 0., c_r = 
-18770011487391973376.


            : x_a =   0., y_a =   0., z_a = 1., c_a =      
  nan


            : x_s =   0., y_s =  -1., z_s = 0., c_s =    
-0.


Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

              0.  -0.      nan        nan

            -0.  -0.      nan        nan

            -0.   0.      nan        nan

              0.   0.   0.     1.

voxel-to-ras determinant nan

ras to voxel transform:

error: mat = NULL!

It appears that this is where the issue is coming from. Any ideas on 
why this is occurring? The brain is normal and has good rh.white and 
rh.pial surfaces.


Many thanks,

Taylor

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 


*Date: *Tuesday, March 5, 2024 at 4:25 PM
*To: *Freesurfer support list 
*Subject: *[EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc 
could not establish read access to rh.area


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Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.


Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ 
directly? Pass full path to your rh.area and rh.area.pial.


What does ‘mri_info rh.area’ report?

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ariko, Taylor

*Sent:* Tuesday, March 5, 2024 2:35 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area


*External Email - Use Caution *

Hello FreeSurfer Developers,

I am attempting