Re: [Freesurfer] xhemi

[Douglas N. Greve]

When creating a laterality-free atlas one needs to make sure to do the 
same thing to the left and right hemi. Eg, the mni152 is not laterally 
symmetric, so you will get a different registration when you register 
your volume directly to the mni152 vs left-right reversing your volume 
and then registering (and why people will register to a symmetric mni152 
when doing such studies). These biases can creep in in other ways. Eg, 
when manually labeling the brain, the labeler might do the left slightly 
different than the right, and this might creep into the atlas (though 
this can be reduced by including left-right reversed labels in the 
atlas). Our standard labels (eg, aparc) are susceptible to these 
problems. Any clearer?


On 3/6/2024 10:52 AM, Joost Janssen wrote:


External Email - Use Caution

Dear Doug,

Thanks. A regional Laterality Index can be calculated using XHEMI (as 
described on the wiki) but also in a different way, e.g. using the 
default FS output from ?h*.stats files and e.g. doing 
(LH-RH)/((LH+RH)/2) or some other formula. You once mentioned about 
this latter approach "But the atlas was not created in a symmetrical 
way, so there might be biases". Could you elaborate on what these 
biases might be?
I read *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767398/ 
 
and it mentions biases when doing registration of a hemisphere to 
either LH or RH but I am not sure if these are the same biases.

Thanks!
-joost

On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve 
 wrote:


Yes, they are. BTW, you should not need to mri_convert the
thickness to mgh format

On 11/27/2023 10:01 AM, Joost Janssen wrote:


External Email - Use Caution

Dear Doug,

The objective is to have _regional_ laterality index for
thickness for aparc mapped to the left hemisphere. The following
commands work without error but are they correct for meeting my
objective? Thanks.

surfreg --s $subject --t fsaverage_sym --lh --no-annot

surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi

mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh

mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh

mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg
$subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg
$subject/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg

mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg
$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg

fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o
$subject/surf/li.thickness.lh.fsaverage_sym.mgh

mri_segstats --annot fsaverage lh aparc --i
$subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum
$subject/stats/li.thickness.aparc.stats

-joost




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

[Kavanaugh, Brian]

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)"

[image: image.png]

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

[image: image.png]

On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing 
wrote:

> It is hard to tell without the data. Is there any output before the core
> dump?
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sennott, Liam
> Ricker
> *Sent:* Wednesday, March 6, 2024 4:28 PM
> *To:* Freesurfer support list 
> *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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <
> yhuan...@mgh.harvard.edu>
> *Date: *Wednesday, March 6, 2024 at 11:05 AM
> *To: *Freesurfer support list 
> *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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
> *Sent:* Wednesday, March 6, 2024 10:57 AM
> *To:* Freesurfer support list 
> *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 -
> https://secure-web.cisco.com/1mpplmqgALrQMWIYrLdz3-T81mClV9RLqIm7McPPGsKuRnj2GZ84HFV-m2wmxmkJ5F593L8IKHZ6sZ0aXD-oWhfy15Bp_Xd7OwdkVBmvVpSKi8WWDeqld0BFIAoDNKizWPhuE2G5HuZftvudh-oEvUhJcnqegcfT3_TP3ZKvuoIidvkW5WDXhEmzC8X_Qo_Hs3sR3msa2y9vowhXlfwNWiuswFZpnOye-0L2s3kPrbLeG9zsuTUy_ti2vaoEgrbTLEZfbCmM4pyT0SpKTovARJbhi48KwmGxudsIgYOh6QRGNps6NRKE4ji8J2aOK0SQ_Pgx40qIepWK3rUepCcTJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_ca_label
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> 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
>
>
>
> *External Email - Use Caution*
>
> 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 anyone have thoughts on how to resolve? I've seen adjacent errors
> before, but none related to ascii specifically.
>
>
>
> thank you!
>
>
>
> brian
>
>
> Brian Kavanaugh, PsyD, ABPP
>
> Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
>
> Assistant Professor, Warren Alpert Medical School of Brown University
> ___
> Freesurfer mailing list
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Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

It is hard to tell without the data. Is there any output before the core dump?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sennott, Liam Ricker
Sent: Wednesday, March 6, 2024 4:28 PM
To: Freesurfer support list 
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 - 
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


External Email - Use Caution
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 anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown University
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Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Sennott, Liam Ricker]

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 
 on behalf of Huang, Yujing 

Date: Wednesday, March 6, 2024 at 11:05 AM
To: Freesurfer support list 
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 
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
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 - 
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


External Email - Use Caution
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 anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown University
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[Freesurfer] Hi

[Farzaneh, Hana]

hfarza...@mgh.harvard.edu

Get Outlook for iOS
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[Freesurfer] Spring 2024 FreeSurfer course

[Sennott, Liam Ricker]

Hello all,



The next virtual FreeSurfer course will be held on April 29th, 30th, and May 
1st.



Registration for this virtual FreeSurfer course is opening on Monday, March 
11th at 12pm Eastern Daylight Time. Visit our course website to find out more 
information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse

Specific questions about the course can be sent to 
fscou...@mgb.org


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

[Huang, Yujing]

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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 8:37 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
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.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area
CAUTION: This email originated from outside the organization. DO NOT CLICK ON 
LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
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

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

[Huang, Yujing]

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 
 On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list 
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 - 
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


External Email - Use Caution
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 anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown University
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Re: [Freesurfer] ascii: bad interpreter: No such file or directory

[Huang, Yujing]

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 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label

Best,

Yujing


From: 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


External Email - Use Caution
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 anyone have thoughts on how to resolve? I've seen adjacent errors before, 
but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP
Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital
Assistant Professor, Warren Alpert Medical School of Brown University
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Re: [Freesurfer] xhemi

[Joost Janssen]

External Email - Use Caution

Dear Doug,

Thanks. A regional Laterality Index can be calculated using XHEMI (as
described on the wiki) but also in a different way, e.g. using the default
FS output from ?h*.stats files and e.g. doing (LH-RH)/((LH+RH)/2) or some
other formula. You once mentioned about this latter approach "But the atlas
was not created in a symmetrical way, so there might be biases". Could you
elaborate on what these biases might be?
I read 
https://secure-web.cisco.com/1TELdMKGVJpKa4ZNA0JT1c2M5j92hscTUXojMSwfCRgHWMi4h330-7qb3M2OGXIYrgOSZICxTxnpti-05ncWdhR6JaJbIx73FVjtEzOdBqK1bpmrufIS7sOC5rf9sTVNVfUF_2k02iDbUNyl8qoOsQMWS5KZS1t7h7JfI_o3K8yrj9LhxQ2EB54r2L_4CsVC3HXfzZQIQW58QvmALvYxzjqKSlL7ZlrmqwXDwD2yTC98P_wzNSIBNXBRqjKkZWOhCZR0piY0tJiFCGuAw6DMfILX-TiwrTwsyjwWmBqI1d_rxSHX5j2-2gRTFnUWbv9ua4qItxp5KwGEhL5PxfcxxZg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3767398%2F
 and it
mentions biases when doing registration of a hemisphere to either LH or RH
but I am not sure if these are the same biases.
Thanks!
-joost

On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve 
wrote:

> Yes, they are. BTW, you should not need to mri_convert the thickness to
> mgh format
>
> On 11/27/2023 10:01 AM, Joost Janssen wrote:
>
> External Email - Use Caution
> Dear Doug,
>
> The objective is to have _regional_ laterality index for thickness for
> aparc mapped to the left hemisphere. The following commands work without
> error but are they correct for meeting my objective? Thanks.
>
> surfreg --s $subject --t fsaverage_sym --lh --no-annot
>
> surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi
>
> mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh
>
> mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh
>
> mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg
> $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg
> $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg
>
> mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg
> $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg 
> $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg
> fsaverage_sym/surf/lh.sphere.reg
>
> fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0
> $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o
> $subject/surf/li.thickness.lh.fsaverage_sym.mgh
>
> mri_segstats --annot fsaverage lh aparc --i
> $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum
> $subject/stats/li.thickness.aparc.stats
>
> -joost
>
>
>
>
> ___
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>  <
> https://secure-web.cisco.com/1cB4DTB7HQw_QfQJKMd9vezQQV6KmmdR6zEjg7Dqj_IsdSoxsubiObgElN9cjhoWNoTo7oJbwxB6abX1drJ1pCrtC5bzoyDOp79zAxUf-6mlLyp7MelGEB01F__dy4PM67pfSJ-JxhGWJnwQBvLkPbEkAoHacBIOd0wRYvr0YIiEqR6Di9WBAoLl-8mBGt1AKtFtzkngmN-W6CXbnxW6zOvyITdJNjrsspktv-ANHBzp3zhaCl44N6NfaWfG2uHK0tL7u-PZ6Jt_G0CxkFg6xRro4A_mstsbzcMiKuhFqA3Q30uk6CLqF5f3SEtnOr8Wxj9pk8JJewnQiYG8J9VI3Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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Re: [Freesurfer] remote access to freesurfer installation...

[Douglas N. Greve]

No, sorry. We do have FS containers that you could use on AWS

On 3/6/2024 9:28 AM, Gonzalo Rojas Costa wrote:


External Email - Use Caution

Hi:

Is there a freesurfer facility where an MRI study can be processed 
remotely?


  Sincerely,


Gonzalo Rojas Costa


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Re: [Freesurfer] Unexpected skull shape after wraped to MNI

[Douglas N. Greve]

Can you be more specific about what abnormality you are seeing? The 
Screenshot2 does not look so bad to me. I'm assuming that this is the 
talairach.xfm transform you are talking about? If so, that is hardly 
used in the stream (and certainly not for placing surfaces), so it is no 
surprise that the results look ok even if the xfm is off a little


On 3/6/2024 5:08 AM, GOFFINET Sara wrote:


External Email - Use Caution

Hello,

I ran freesurfer recon_all on a T1 MRI sequence (you can find the orig 
T1 in Screenshtot1) and my participant's brain warped to MNI 
(worig.nii) looks deformed (Screenshot2). Do you know why is there a 
bump (the worig file does not overlay well on MNI) while the 
reconstruction of the pial surface (lh.pial, rh.pial) shows no 
abnormality?



Thanks in advance,


Sara Goffinet


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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means that 
the surface placement algorithm is pushing the surface into subcortical 
gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:


External Email - Use Caution

Yes, the problem is that the white surface on the left side of the 
image is extending too far into subcortical gray matter. We did delete 
the control points and ran some white matter edits, but the image I 
sent you is after we applied those edits (it was even worse before). I 
don’t see any other wm edits we can make to the image. It didn’t 
resolve our issue enough to make the image usable for our analyses, so 
I wanted to see if there was anything else we could do to resolve the 
problem.


Thank you!

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


*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white surface 
on the left side of the image is extending too far into subcortical 
gray matter, right? This can be difficult to fix, but the right fix is 
to edit the wm.mgz. Make sure to delete your control points as that is 
not the right fix. Also, remember that the surfaces in this area may 
always be inaccurate if you can see where the boundary is.


On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image

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

 on behalf of
Douglas N. Greve 

*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu


*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without errors),
except 4 images which have an underestimation in coronal
subcortical region. The underestimation is significant and
goes on for about 10-12 slices (for one image it was 153-162,
for another it was 150-164).

After searching the list, we attempted control points, which
ended up not working (I don’t believe this was the right
method to correct the error). Then we tried white matter
edits, and one of the images was resolved, but the other 3 did
not get better. Is there anything else we could do to try to
resolve the issue? I can provide any other information needed.
Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image

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[Freesurfer] remote access to freesurfer installation...

[Gonzalo Rojas Costa]

External Email - Use Caution

Hi:

  Is there a freesurfer facility where an MRI study can be processed
remotely?

  Sincerely,


Gonzalo Rojas Costa
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[Freesurfer] ascii: bad interpreter: No such file or directory

[Kavanaugh, Brian]

External Email - Use Caution

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 anyone have thoughts on how to resolve? I've seen adjacent errors
before, but none related to ascii specifically.

thank you!

brian

Brian Kavanaugh, PsyD, ABPP

Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital

Assistant Professor, Warren Alpert Medical School of Brown University
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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

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.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
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
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area
CAUTION: This email originated from outside the organization. DO NOT CLICK ON 
LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
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
 
mailto: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 to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
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 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

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