Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

[Lara Foland-Ross]

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Sure. Here's the output:

sh-4.2# mri_info mri/rawavg.mgz 
Volume information for mri/rawavg.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
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 = 5.3997
  : x_a =   0., y_a =   0., z_a =   1., c_a =18.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   133.3997
0.   0.   1.  -110.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   133.3997
   -0.  -0.  -1.   128.
   -0.   1.  -0.   110.
   -0.  -0.  -0. 1.


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

Sent: Monday, May 10, 2021 12:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

Can you run
mri_info  /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz

On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:

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Hello,

I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple 
chip with BigSur as the OSX.

To test out the installation, I ran recon-all on bert:

recon-all -all -s bert

The command quits with this error:

"ERROR: cannot determine file type for 
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021"

I'm attaching the recon-all.log file.

Could you please advise on how to troubleshoot?

Many thanks,
Lara





Lara Foland-Ross, Ph.D.
Senior Research Associate and Imaging Lab Manager
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795




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Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

[Douglas N. Greve]

Can you run
mri_info  /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz

On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:

 External Email - Use Caution

Hello,

I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple 
chip with BigSur as the OSX.

To test out the installation, I ran recon-all on bert:

recon-all -all -s bert

The command quits with this error:

"ERROR: cannot determine file type for 
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021"

I'm attaching the recon-all.log file.

Could you please advise on how to troubleshoot?

Many thanks,
Lara





Lara Foland-Ross, Ph.D.
Senior Research Associate and Imaging Lab Manager
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795

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Re: [Freesurfer] Error in SAMSEG preprocessing

[Hoopes, Andrew]

If this is the last message before crashing, it sounds like it’s probably a 
memory issue – how much do you have available? CC’ing Stefano who might have an 
idea of the total memory requirement for lesions.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Monday, May 10, 2021 at 9:31 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution
After 14th interaction the terminal wrote this message:

I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports 
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-05-10 13:40:01.273046: I 
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 
3292375000 Hz
2021-05-10 13:40:01.281440: I tensorflow/compiler/xla/service/service.cc:150] 
XLA service 0x30013a0 executing computations on platform Host. Devices:
2021-05-10 13:40:01.281470: I tensorflow/compiler/xla/service/service.cc:158]   
StreamExecutor device (0): , 
WARNING:tensorflow:From 
/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266:
 checkpoint_exists (from tensorflow.python.training.checkpoint_management) is 
deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
VAE lesion model loaded
2021-05-10 13:40:16.471711: W tensorflow/core/framework/allocator.cc:124] 
Allocation of 171720 exceeds 10% of system memory.

I tried to improve the system memory of my virtual machine but the same error 
appeared.

Any suggestions?


El vie, 7 may 2021 a las 20:59, Hoopes, Andrew 
(mailto:ahoo...@mgh.harvard.edu>>) escribió:
If the output directory is missing seg.mgz, then samseg failed. You’ll have to 
send us the log or some sort of information about the error for us to debug 
this.

Best
Andrew

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alberto Del Cerro Leon 
mailto:bertocer...@gmail.com>>
Date: Friday, May 7, 2021 at 6:49 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in SAMSEG preprocessing

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Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the 
following command:

run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' 
'/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion 
--lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/'

The output files were:

  *   cost.txt
  *   priors-testing.mgz
  *   samseg.talairach.lta
  *   template.lta
  *   template_coregistered.mgz
  *   template_transforms.mat
However I don't find any file with the white matter lesions segmented or a stat 
file. I would send you the terminal outputs but is too extensive. Would you 
help me?
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Re: [Freesurfer] mri_ribbon does not return the ribbon

[Douglas N. Greve]

You can try using mri_surf2vol. Run with --help and use method1

On 5/10/2021 12:54 PM, Caspar M. Schwiedrzik wrote:


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Hi Doug,
Thank you - we tried this. We do not have aseg and therefore 
mris_volmask will not do it.

Caspar

On Mon, May 10, 2021 at 18:09 Douglas N. Greve > wrote:


Try
cd yoursubjectname/mri
mris_volmask  --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
yoursubjectname


On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:


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Hi!
I am trying to make a ribbon.mgz from a non-human primate surface
recon that does not have an aseg. Following this prior
discussion: *MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be* Re: [Freesurfer]
ribbon.mgz Without aseg.mgz (mail-archive.com)


I tried mri_ribbon:
mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
rh.ribbon.mgz
Attached is the output. It looks like it roughly follows the grey
matter, but especially the sulci seem to be filled.
Unfortunately, there is no help for mri_ribbon. Any advice on how
to proceed? The above mentioned discussion did not lead to a
conclusion on how to get a ribbon without aseg.
Thank you! Caspar


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Re: [Freesurfer] mri_ribbon does not return the ribbon

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi Doug,
Thank you - we tried this. We do not have aseg and therefore mris_volmask
will not do it.
Caspar

On Mon, May 10, 2021 at 18:09 Douglas N. Greve 
wrote:

> Try
> cd yoursubjectname/mri
> mris_volmask  --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname
>
>
> On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am trying to make a ribbon.mgz from a non-human primate surface recon
> that does not have an aseg. Following this prior discussion: *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)
> 
> I tried mri_ribbon:
>
> mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
> rh.ribbon.mgz
>
> Attached is the output. It looks like it roughly follows the grey matter,
> but especially the sulci seem to be filled. Unfortunately, there is no help
> for mri_ribbon. Any advice on how to proceed? The above mentioned
> discussion did not lead to a conclusion on how to get a ribbon without
> aseg.
> Thank you! Caspar
>
>
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Re: [Freesurfer] Απ: volume ROI to surface for cortical thickness

[Douglas N. Greve]

For when your ROI is in fsaverage (or MNI152) space.

On 5/10/2021 12:34 PM, M Pope wrote:


External Email - Use Caution

External Email - Use Caution

The labels are derived from ASHS- but yes they are registered to each 
subject seperately. Could I ask then what the tutorial refers to- for 
future reference? When is it best to go through fsaverage?


Thank you for the information

BW,
Marianna



*Από:* freesurfer-boun...@nmr.mgh.harvard.edu 
 εκ μέρους του Douglas N. 
Greve 

*Στάλθηκε:* Δευτέρα, 10 Μαΐου 2021 4:30 μμ
*Προς:* freesurfer@nmr.mgh.harvard.edu 
*Θέμα:* Re: [Freesurfer] volume ROI to surface for cortical thickness
did you draw the labels on each subject separately? In that case there 
is no need to go through fsaverage.
Projfrac is the fractional distance between the white and pial 
surfaces (0.5 is half way)

projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts to changes in thickness
In your case, you might want to use --projfrac-max where it will look 
over a range of projfrac values for the maximum. This might make your 
maps look better because it will be sampling the label or nothing.


On 5/10/2021 12:25 PM, M Pope wrote:


External Email - Use Caution

External Email - Use Caution

Dear Freesurfer experts,

I have created volumetric ROIs of entorhinal cortex regions and have 
registered them to subjects’ native space (T1). I now wish to 
register them to the subject surface in order to get information such 
as cortical thickness- using mri_vol2surf and mri_segstats I believe.


I was looking at your tutorial regarding this 
VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu) 
 and 
had a few questions.


First of all- could you explain why you are going through fsaverage. 
Is there some kind of advantage to doing this procedure of 
registration, mri_vol2surf and then mri_surf2surf rather than just 
using mri_vol2surf with the subject space as the regheader?? When I 
tried through fsaverage as explained in the tutorial (following the 
exact same commands) the ROI appeared wrong in the surface and the 
thickness stats were incorrect.


Secondly, when doing the procedure as per the tutorial, do you mean 
that we have to register each subject's mask to the fsaverage- or 
only one, e.g a ROI derived from the subject-specific group template 
(we have one produced through ANTs).


Lastly- some explanation about how projfrac and projdist work would 
be very helpful. What numbers are considered best practice?


Thankyou,

Marianna Pope



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[Freesurfer] Απ: volume ROI to surface for cortical thickness

[M Pope]

External Email - Use Caution

The labels are derived from ASHS- but yes they are registered to each subject 
seperately. Could I ask then what the tutorial refers to- for future reference? 
When is it best to go through fsaverage?

Thank you for the information

BW,
Marianna



Από: freesurfer-boun...@nmr.mgh.harvard.edu 
 εκ μέρους του Douglas N. Greve 

Στάλθηκε: Δευτέρα, 10 Μαΐου 2021 4:30 μμ
Προς: freesurfer@nmr.mgh.harvard.edu 
Θέμα: Re: [Freesurfer] volume ROI to surface for cortical thickness

did you draw the labels on each subject separately? In that case there is no 
need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces (0.5 is 
half way)
projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts to changes in thickness
In your case, you might want to use --projfrac-max where it will look over a 
range of projfrac values for the maximum. This might make your maps look better 
because it will be sampling the label or nothing.

On 5/10/2021 12:25 PM, M Pope wrote:

External Email - Use Caution

External Email - Use Caution

Dear Freesurfer experts,



I have created volumetric ROIs of entorhinal cortex regions and have registered 
them to subjects’ native space (T1). I now wish to register them to the subject 
surface in order to get information such as cortical thickness- using 
mri_vol2surf and mri_segstats I believe.



I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free 
Surfer Wiki 
(harvard.edu)
 and had a few questions.

First of all- could you explain why you are going through fsaverage. Is there 
some kind of advantage to doing this procedure of registration, mri_vol2surf 
and then mri_surf2surf rather than just using mri_vol2surf with the subject 
space as the regheader?? When I tried through fsaverage as explained in the 
tutorial (following the exact same commands) the ROI appeared wrong in the 
surface and the thickness stats were incorrect.

Secondly, when doing the procedure as per the tutorial, do you mean that we 
have to register each subject's mask to the fsaverage- or only one, e.g a ROI 
derived from the subject-specific group template (we have one produced through 
ANTs).

Lastly- some explanation about how projfrac and projdist work would be very 
helpful. What numbers are considered best practice?



Thankyou,

Marianna Pope




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Re: [Freesurfer] volume ROI to surface for cortical thickness

[Douglas N. Greve]

did you draw the labels on each subject separately? In that case there 
is no need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces 
(0.5 is half way)

projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts to changes in thickness
In your case, you might want to use --projfrac-max where it will look 
over a range of projfrac values for the maximum. This might make your 
maps look better because it will be sampling the label or nothing.


On 5/10/2021 12:25 PM, M Pope wrote:


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Dear Freesurfer experts,

I have created volumetric ROIs of entorhinal cortex regions and have 
registered them to subjects’ native space (T1). I now wish to register 
them to the subject surface in order to get information such as 
cortical thickness- using mri_vol2surf and mri_segstats I believe.


I was looking at your tutorial regarding this 
VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu) 
 and 
had a few questions.


First of all- could you explain why you are going through fsaverage. 
Is there some kind of advantage to doing this procedure of 
registration, mri_vol2surf and then mri_surf2surf rather than just 
using mri_vol2surf with the subject space as the regheader?? When I 
tried through fsaverage as explained in the tutorial (following the 
exact same commands) the ROI appeared wrong in the surface and the 
thickness stats were incorrect.


Secondly, when doing the procedure as per the tutorial, do you mean 
that we have to register each subject's mask to the fsaverage- or only 
one, e.g a ROI derived from the subject-specific group template (we 
have one produced through ANTs).


Lastly- some explanation about how projfrac and projdist work would be 
very helpful. What numbers are considered best practice?


Thankyou,

Marianna Pope



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[Freesurfer] volume ROI to surface for cortical thickness

[M Pope]

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Dear Freesurfer experts,

I have created volumetric ROIs of entorhinal cortex regions and have registered 
them to subjects’ native space (T1). I now wish to register them to the subject 
surface in order to get information such as cortical thickness- using 
mri_vol2surf and mri_segstats I believe.

I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free 
Surfer Wiki 
(harvard.edu)
 and had a few questions.

First of all- could you explain why you are going through fsaverage. Is there 
some kind of advantage to doing this procedure of registration, mri_vol2surf 
and then mri_surf2surf rather than just using mri_vol2surf with the subject 
space as the regheader?? When I tried through fsaverage as explained in the 
tutorial (following the exact same commands) the ROI appeared wrong in the 
surface and the thickness stats were incorrect.

Secondly, when doing the procedure as per the tutorial, do you mean that we 
have to register each subject's mask to the fsaverage- or only one, e.g a ROI 
derived from the subject-specific group template (we have one produced through 
ANTs).

Lastly- some explanation about how projfrac and projdist work would be very 
helpful. What numbers are considered best practice?

Thankyou,
Marianna Pope

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Re: [Freesurfer] Register Hippocampus mask to T1.nii

[Douglas N. Greve]

You should not need to. The files with the string .FSvoxelSpace in them 
should already be in that space


On 5/10/2021 5:32 AM, Borghi, G. (Gregorio) wrote:


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Dear All,


Due to my study, I have been unsuccessfully trying to co-register the 
hippocampal and amygdala segmented file (obtained from 
segmentHA_T2.sh) to my T1-weighted anatomical image (.nii), so that I 
can use the segmented file as a mask for later ROI analysis. However, 
despite trying in several ways with mri_robust_register 
and tkregister2, I have not been able to coregister the 2 together. 
Any suggestions?



Kind regards,
Greg
s1034199

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Re: [Freesurfer] Gyrification group comparison - GLM

[Douglas N. Greve]

lGI has a lot of native smoothness in it, often so much that it exceeds 
the tables that we precompute. I would strongly suggest not using the 
precomputed tables for this and instead use permutation. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm


On 5/9/2021 5:13 PM, Georgia Kapizioni wrote:


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Dear FS experts,

I am running a GLM for a group comparison (Healthy versus Patients) 
for gyrification, using the following command:


mri_glmfit --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C 
Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir 
lh.HDcvsCons1_pial.glmdir


which seems to work fine, however when I am running the mri_glmfit-sim 
command to correct my results, I am getting the following error, which 
is strange as I use smoothed data of 10 fwhm.


Do you have any ideas why is this happening and how to resolve it?

Thank you in advance,
Best,
Geo

mri_glmfit-sim --glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs 
--cwp .05 --2spaces
cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd 
HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex 
--glmdir lh.HDcvsCons1_pial.glmdir

SURFACE: fsaverage lh
log file is lh.HDcvsCons1_pial.glmdir/cache.mri_glmfit-sim.log

cd /Users/georgina/Downloads/HDf
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs --cwp .05 --2spaces

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Mon May 10 00:10:37 EEST 2021
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: 
Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64

georgina
setenv SUBJECTS_DIR /Users/georgina/Downloads/HDf
FREESURFER_HOME /Applications/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd 
HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex 
--glmdir lh.HDcvsCons1_pial.glmdir


DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 43.252960
ERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm43/abs/th13/mc-z.csd


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Re: [Freesurfer] mri_preproc with ico < 7?

[Douglas N. Greve]

You should be able to use --target fsaverage5 (or fsaverage4)


On 5/9/2021 3:54 PM, Knut J Bjuland wrote:


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Dear Freesurfer experts,

 Is it possible to run mri_preproc with ico with lower than 7, for 
instance with ico equal to 4 or 5 in order to downsample the surface? 
(Since the surface is smoothed, it should be possible to downsample to 
save processing time when doing statistical modelling, right?) I tried 
using an --ico or --icoorder flag, but just got an error message. Are 
these functions not continued? Thank you



 Your Sincerely
 Knut Jørgen Bjuland, PhD

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Re: [Freesurfer] FA map registration to T1

[Douglas N. Greve]

I took a look at the data. It looks like pretty large B0 distortion to 
me (just look at the eye balls). If you don't have a B0 map, then 
there's not much you can do.


On 4/26/2021 8:29 AM, Russo, Andrew William wrote:
We don't have B0 fieldmap data, would I still be able to perform this 
correction? For preprocessing we ran eddy_openmp and dtifit.


The helpdesk has added klawms to your sudo groups for access to the 
data. Please let me know if you need any more information.


Thanks so much for your help,
Andrew

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


*Sent:* Sunday, April 25, 2021 10:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] FA map registration to T1
Everything looks ok in the log file. Did you do an B0 distortion 
correction? Can you give me access to that data?


On 4/20/2021 10:34 AM, Russo, Andrew William wrote:

Log file is attached.

Thank you,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531

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

*Sent:* Tuesday, April 20, 2021 10:09 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] FA map registration to T1
can you send the bbr log file?

On 4/19/2021 2:29 PM, Russo, Andrew William wrote:

Hello FreeSurfer Developers,

I am registering FA maps to T1 for a group of subjects with MS and 
in many cases the registration is poor for the anterior corpus 
callosum (attached), cerebellum, pons, and temporal lobe. I am using 
the following commands (FreeSurfer version 6.0):


bbregister \
    --dti \
    --reg diff2T1_reg.dat \
    --mov eddy_corrected_b0.nii.gz \
    --s subject_temp

mri_vol2vol \
    --mov dtifit_FA.nii.gz \
    --targ orig.mgz \
    --o FA2T1.nii.gz \
    --reg diff2T1_reg.dat

Do you have any suggestions for improving this registration?

Thank you,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531

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Re: [Freesurfer] Registering preop and postop MRI scans

[Douglas N. Greve]

Can you be more specific that "weren't really good"?

On 5/6/2021 12:03 PM, Peled, Noam wrote:


Dear group,

I have preop and postop MRI scans of an epileptic patient.

I ran recon-all on the preop, and bbregister on the postop to register 
it to the preop.


I’m not sure why, but the results weren’t really good.

Maybe I should try using the longitudinal pipeline?

Thanks,

Noam


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Re: [Freesurfer] mri_ribbon does not return the ribbon

[Douglas N. Greve]

Try
cd yoursubjectname/mri
mris_volmask  --label_left_white 2 --label_left_ribbon 3 
--label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname



On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:


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Hi!
I am trying to make a ribbon.mgz from a non-human primate surface 
recon that does not have an aseg. Following this prior discussion: 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* Re: [Freesurfer] ribbon.mgz 
Without aseg.mgz (mail-archive.com) 
 
I tried mri_ribbon:

mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
rh.ribbon.mgz
Attached is the output. It looks like it roughly follows the grey 
matter, but especially the sulci seem to be filled. Unfortunately, 
there is no help for mri_ribbon. Any advice on how to proceed? The 
above mentioned discussion did not lead to a conclusion on how to get 
a ribbon without aseg.

Thank you! Caspar


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Re: [Freesurfer] mri_label2_vol missing grey matter voxels

[Douglas N. Greve]

A better way to do this is to use mri_surf2volseg. Look in the 
recon-all.cmd file for your subject and find the command that creates 
the aparc+aseg.mgz file. Use that command but changing the annot file 
and output file


On 5/6/2021 8:12 AM, Nakajima, Mitsuko wrote:


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Dear FreeSurfer Developers,

I am trying to extract the cortical ROIs from my subjects.

(1) mri_surf2surf, transform from fsaverage surface with Glasser atlas 
annotation, onto the subject surface.
(2) mri_label2vol, transform from the subject's surface (labelled with 
the Glasser atlas) onto subject's volume.


# Step 1: Transform from fsaverage to subject's surface (Ensure 
fsaverage contains HCP-MMP1.annot in labels folder)
$ mri_surf2surf --srcsubject scripts/fsaverage --trgsubject 
${i}/${sub} --hemi lh --sval-annot HCP-MMP1.annot --tval 
lh.HCP-MMP1_native.annot


# Step2: Transform from subject's surface into your subject's volume
$ mri_label2vol --temp ${SUBJECTS_DIR}/${i}/${sub}/mri/brain.mgz 
--annot HCP-MMP1_native.annot --o 
${SUBJECTS_DIR}/${i}/${sub}/lh_native_glasser.nii.gz --hemi lh 
--subject ${i}/${sub} --regheader 
${SUBJECTS_DIR}/${i}/${sub}/mri/aseg.mgz --proj frac 0 1 .1 
--fillthresh .3


However, the output image shows pixelated grey matter.
I've tried using different --filthresh, but the appearance remains the 
same.
Please find attached the screenshot of the output, as well as the 
recon-all log.


I've looked through the list, and I did not find a solution to a case 
that I can apply to my situation.


1) Freesurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
2) Platform: Mac OS X Mojave, 10.14.6
3) recon-all log as attached

Thank you so much for your help.

Kind regards,
Mitsuko

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Re: [Freesurfer] error while running mri_glmfit-sim command

[Douglas N. Greve]

It is trying to find a precomputed table of p-values based on the 
criteria of your particular analysis. However, The smoothness of your 
data is extreme, and the tables were not computed for such smooth data. 
What is the nature of your data?


On 5/5/2021 11:29 AM, Paul, Rahul wrote:

Hi Freesurfer Experts,

I am having some error while running mri_glmfit-sim command

ERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm56/abs/th20/mc-z.csd


I was using the following command:
mri_glmfit-sim   --glmdir lh.class2_age.glmdir   --cache 4 abs --cwp 
 0.05 --2spaces


How can I fix the error?

Thank you,

Rahul

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Re: [Freesurfer] Extracting the entire brain mask from aparc+aseg.mgz

[Douglas N. Greve]

You can use use mri_binarize with --min 0.5 and it will take all labels 
with value 1 and greater. You can create a bounding box with mri_mask 
with the -bb option


On 5/4/2021 11:53 AM, Arman Avesta wrote:


External Email - Use Caution

Hi gang,

I have downloaded head MRIs of 1000 subjects from ADNI, together with 
their FreeSurfer generated aparc+aseg.mgz files. I'm using them in a 
3D deep learning network. These MRIs are 256 x 256 x 256, which is too 
large for GPU training. Therefore, I'm trying to pre-process the 
volumes by putting a bounding box around the brain, crop the image, 
and then resize it to a smaller size (e.g. 64 * 100 * 100).


To put the bounding box around the brain, I need the brain mask. I 
don't have access to the brainmasks of these subjects, so I'm trying 
to use mri_extract_label to make brainmasks for them.


Is there a way to tell mri_extract_label to put together all labels in 
one volume?


Best regards,

Arman




*Arman Avesta, MD*
Radiology Resident & PhD Student
Yale School of Medicine & Yale Graduate School of Arts and Sciences

Email: arman.ave...@yale.edu


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Re: [Freesurfer] PET seeding with hippocampal subfields

[Douglas N. Greve]

REgister the FDG to the anatomical (mri_coreg --s subject --mov fdg.nii 
--reg fdg.reg.lta), sample the FDG into the anatomical space 
(mri_vol2vol --mov fdg.nii --reg fdg.reg.lta --fstarg --o fdg.anat.mgz), 
the use mri_segstats --seg 
rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i fdg.anat.mgz --sum 
sum.dat



On 5/3/2021 12:48 PM, Mohammad Akradi wrote:


External Email - Use Caution

Dear Freesurfer Development Team

I've used freesurfer with hippocampal subfields module to get GM and 
Thickness in this region in detail. but now I need this subfields' 
mask to use it on my PET data. So I'll appreciate it if you tell me 
how I can get this regions' mask. Or which atlas I should use to 
achieve them? so I can calculate FDG uptake in these regions too.


best regards

--
Mohammad Akradi
MSc Student,
Institute of Medical Science and Technology,
Shahid Beheshti University, Tehran, Iran

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Re: [Freesurfer] Cluster correction at subject level using -log10(p) values

[Douglas N. Greve]

Is there a reason that you are not using mri_glmfit-sim to do this? It 
is fairly complicated, and so I spent a lot of time writing 
mri_glmfit-sim to make sure it does the right thing.


On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:


External Email - Use Caution

Dear Experts,

I am running an analysis where I have -log10(p) values on the cortical 
surface of some subjects stored as a MGH file.


I would now like to run a cluster level correction on these data at 
the level of each individual subject using mri_mcsim followed by 
mri_surfcluster and I would like to constrain my inference to a ROI.


I have a few questions. First of all, is it correct that I should to a 
-log10(p) transform on my p values before entering them in 
mri_surfcluster?


Second, will the csd generated by mcsim be valid to feed in 
mri_surfcluster since the values are a -log10(p) transformed? Does 
mcsim -log transform the gaussian noise it uses at some point or is 
this not necessary?


My calls to the two methods are as follows (for one hemisphere):

First the mcsim:

mri_mcsim --o“${subject}_mcsim_lh_${roi}"--basemc-z 
--surface${subject}lh --nreps1--label$roi


Then the mri_surfcluster:

mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \

--csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \

--clabel "${subject}/label/lh.${roi}.label" \

--cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \

--vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \

--sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \

--thmin 3 \

--surf white \

--subject ${subject } \

--hemi lh \

--ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \

--cwpvalthresh 0.05

In the call of mri_surfcluster, I want a cluster forming threshold of 
p=0.001, which would correspond to -logp(0.001)=3. Is it correct that 
the argument --thmin should be expressed as -log10(p) but the 
parameter cwpvalthresh should be p?


The reason why I think I did something wrong is that I get a lot of 
clusters from this analysis, sometimes >15 per individual. This makes 
me think that the correction might not be as stringent as I would like 
to.


Thank you,

Leonardo Tozzi, MD, PhD

Williams PanLab | Postdoctoral Researcher

Stanford University | 401 Quarry Rd

lto...@stanford.edu  | (650) 5615738

*/Connect with us!/*

signature_1075933358 
signature_1282923475 
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Re: [Freesurfer] Cortical surface analysis

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

On 4/28/2021 5:18 PM, Fischl, Bruce wrote:


Yes, there is some documentation of how to do this on our website. I 
defer to Doug on the particulars


Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Ornaith O Reilly

*Sent:* Wednesday, April 28, 2021 4:30 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Cortical surface analysis

*External Email - Use Caution *

Hi Bruce,

Thanks a lot for this.  What is the difference between RAS and surface 
RAS?


Do I need to convert the surface RAS into RAS to be dealing in the 
volume space?


Kind Regards,

Ornaith

On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce > wrote:


All the surface vertices are just listed in order. The patch keep
track of which vertex it corresponds to (so you can just use
pial_surface[patch.vno] or something).

The coordinates are documented on our website and are “surface ras”.

Cheers

Bruce

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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Ornaith O Reilly
*Sent:* Tuesday, April 27, 2021 8:02 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis

*External Email - Use Caution *

Hi Bruce,

Yes I read in the patch the way that you're suggesting and I can
access the vino for the flat map.  But how do i know the vertex
number of each vertex in the pial surface?  Are they in order ?

Also, what coordinate system is the pial surface in when its read
into FreeSurfer? Is it RAS or surface RAS?

Kind Regards,

Ornaith

On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:

How do you read it in? If you are using the read_patch.m that
we distribute it should be stored in patch.vno if you do:

>> patch = read_patch(path_file_name)

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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Ornaith O Reilly
*Sent:* Wednesday, April 7, 2021 2:29 PM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis

*External Email - Use Caution *

Hi Bruce,

Thanks so much for your quick reply, I really appreciate your
help on this.

I don't understand how to recover the vertex index.

In Freeview I can see the vertex index number.  When I load in
the data to MATLAB as discussed - the only thing that I have
access to are the coordinates of the vertices - not the vertex
index.  How can I recover the vertex indices as well?

Thanks again.

Kind Regards,

Ornaith

On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:

Hi Ornaith

The mapping uses the vertex index. That is, the vertex
index is stored in the flatmap, so you should always be
able to recover it, then look up the location of that
vertex on any other surface (of the same hemisphere/subject)

Cheers

Bruce

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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On
Behalf Of *Ornaith O Reilly
*Sent:* Tuesday, April 6, 2021 2:19 PM
*To:* Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Cortical surface analysis

*External Email - Use Caution *

Hello FreeSurfer developers,

Thanks a lot for your help.  I have initialised the
pialxyz the way you suggested and made the flatmap in
MatLab using the read_patch function (screenshots
attached). I still don't understand how to convert
between the two.  For example how to see what point
(x,y,z) on the pial surface corresponds to what (x,y)
point on the flatmap.

Thanks a lot for your help.

Kind Regards,

Ornaith

On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

On 3/8/2021 11:38 AM, Ornaith O Reilly wrote:

*External Email - Use Caution *

Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone
can help me.

My 

Re: [Freesurfer] Cannot select ROI edit tool in Freeview

[Douglas N. Greve]

your description is unclear to me

On 4/28/2021 12:23 PM, Mercy Mazurek wrote:


External Email - Use Caution

I loaded my brainmask.mgz file generated from a "recon-all 
-autorecon1" command. When I open up Freeview, I see the icon but it 
is grayed out and I cannot select it to create a volume ROI on my 
image. How do I draw an ROI on my scans?


Thanks for your help!

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Re: [Freesurfer] GM Volumes

[Douglas N. Greve]

look in ?h.aparc.stats files

On 4/27/2021 2:17 PM, Nils B. wrote:


External Email - Use Caution

Dear Freesurfer developers,

I'm hoping you can help me once again.
Right now I'm working on how to extract certain measurements out of my 
data set. I have two groups and MRI data from one time point in 
elderly people. The data quality is pretty bad but for pilot analysis 
I want to analyze the gray matter volume difference in some ROI's. 
I've already found the total GM volume in the aseg-stats as well as 
the hippocampal volumes but I couldn't find any of these ROI's:
subiculum, parahippocampal gyrus,Central sulcus, Cingulate cortex, 
left frontal cortex, central premotor cortex, ventral premotor cortex.


Are any of these regions found in the Freesurfer output or is there a 
way to generate them? Has Freesurfer even a way to automatically 
identify these regions?


My Set-up:
Freesurfer Version: 7.1
Plattform: Ubuntu 18.04

Thank you in advance for the help!

Best regards,

Nils
--

Nils Böer
Research Assistant with Bachelor Degree (WHB)
*Psychology and Movement Science*
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de 

Web: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ 

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://sug.uni-paderborn.de/department/it/ 



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Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to surface

[Douglas N. Greve]

You can use mri_segstats on the output to get your table of values for 
each ROI. Run it with --help and see example 5


On 4/27/2021 1:50 PM, Jensen, Alexandria wrote:


External Email - Use Caution

I believe I have using the code below, though I am not fully certain 
of it:


bbregister \

--s freesurfer \

--mov odi.nii \

--init-fsl \

--reg register.dat \

--dti


tkregister2 \

--s freesurfer \

--mov odi.nii \

--reg register.dat \

--surf

mri_vol2surf \

--src odi.nii \

--out odi_in_cortexL.nativespace.mgh \

--srcreg register.dat \

--hemi lh \

--projfrac 0.5



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


*Sent:* Monday, April 26, 2021 5:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps 
inflated to surface


Oh, then you don’t need -l at all I don’t think. Have you sampled your 
ODI file onto the surface?


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

*Sent:* Monday, April 26, 2021 5:01 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps 
inflated to surface


*External Email - Use Caution *

Hi Bruce,

Thank you for the help! If the -a option is the aparc.DKTatlas.annot 
file and the -l option should be a label file, where does the ODI 
surface file come into play? My ultimate goal is to get average ODI 
values for each ROI in the DKT atlas.


Alexandria



*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 
> on behalf of Fischl, 
Bruce mailto:bfis...@mgh.harvard.edu>>

*Sent:* Monday, April 26, 2021 2:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps 
inflated to surface


Hi Alexandria

The file given in the -l option should be an ascii label file, not a 
volume.


Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
> *On Behalf Of 
*Jensen, Alexandria

*Sent:* Monday, April 26, 2021 4:26 PM
*To:* freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps 
inflated to surface


*External Email - Use Caution *

This is the command I use for mris_anatomical_stats and the terminal 
output. I have taken out some of the directory information for privacy 
reasons.


mris_anatomical_stats \

-a /.../freesurfer/label/lh.aparc.DLTatlas.annot \

-l odi_in_cortexL.nativespace.mgh \

-b subject_xxx \

lh

computing statistics for each annotation in 
/…/freesurfer/label/lh.aparc.DKTatlas.annot.


limiting computations to label ODI_in_cortexL.nativespace.mgh.

reading volume /…/freesurfer/mri/wm.mgz...

reading input surface /… /freesurfer/surf/lh.white...

Using TH3 vertex volume calc

Total face volume 227931

Total vertex volume 224122 (mask=0)

reading input pial surface /… /freesurfer/surf/lh.pial...

reading input white surface /…/freesurfer/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) 



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

*Sent:* Sunday, April 25, 2021 8:35 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps 
inflated to surface


what is your mris_anatomical_stats command and terminal output?

On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:

*External Email - Use Caution *

Hello fellow Freesurfer users,


  I am attempting to reproduce the analysis conducted by Parker et
  al. in their 2018 paper, “Cortical microstructure in young onset
  Alzheimer's disease using neurite orientation dispersion and
  density imaging” (*MailScanner has detected a possible fraud
  attempt from "secure-web.cisco.com" claiming to be*
  https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24056
  

Re: [Freesurfer] Extract ROI cortical thickness with mri_segstat

[Douglas N. Greve]

Significant in group analysis of what? The commands look ok

On 4/27/2021 9:18 AM, LIN, Yezhe wrote:


External Email - Use Caution

Dear Freesurfer experts,

My name is Yezhe Lin. I am trying to extract the thickness in an area 
we found significant in group analysis. However, when we did a t-test 
on the extracted values, the significance was not obtained. I wonder 
something could go wrong somewhere and what possibly caused the 
difference. I attached my scripts for the adjusted pipeline FYI.



steps
#make a 3x3x3 ROI using the peak coordinate obtained in group analysis 
in standard space (MNI152) by fslview


#check ROI location
tkmedit -f /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz 
-overlay MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii -fthresh 0.5

# register to fsaverage of the dataset
cd ../fsaverage/surf/ (Freesurfer_Home fsaverage)
fslregister --s fsaverage --mov 
/mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii 
--reg MNI2mm_to_fsaverage.dat

#To check results, run:
tkregister2 --mov 
/mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii 
--reg MNI2mm_to_fsaverage.dat --surf orig
#view your ROI in the fsaverage subject volume to ensure that it is 
located where you expect it to be: (two pials clear)

cd $SUBJECTS_DIR/fsaverage/surf
 tkmedit fsaverage T1.mgz \
  -overlay 
/mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii 
\

  -overlay-reg MNI2mm_to_fsaverage.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white

#register ROI to fsaverage space
cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
  --mov 
/mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii 
\

  --reg MNI2mm_to_fsaverage.dat \
--projdist-max 0 1 0.1 \
  --interp nearest \
  --hemi rh \
  --out rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh
#view the ROI registration (on the peak center of significant cluster)

tksurfer fsaverage rh inflated -overlay 
rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh -fthresh 0.5


# extract values from rh.XXX.CBPvsHC_age_sex_eTIV.10.mgh
mri_segstats --i ../rh.thickness.CBPvsHC_age_sex_eTIV.10.mgh --seg 
rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh --excludeid 0 --avgwf 
CBPHC_th_results.dat



Hope my questions is clear! Appreciate your kind help and time!


--

Best regards,

Yezhe

Yezhe Lin, MD MMed  (she/her/hers)

Postdoctoral Associate, Department of Psychiatry

University of Rochester Medical Center

yezhe.lin@gmail.com

Twitter 
: 
@LinYezhe | LinkedIn 
 | 
Researchgate 




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Re: [Freesurfer] mask error in glm_fit

[Douglas N. Greve]

It is saying that the mask lhYeo2011_7NetworksConfidence_N1000.mgzdoes 
not have thee same dimensions as the input. How was it created? It must 
be a surface overlay on fsaverage


On 4/26/2021 6:59 PM, Haley Park wrote:


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Hello,

I am trying to run a correlational analysis with glm_fit on a masked 
area with the code:


foreach hemi (lh)

foreach smoothness (10)

foreach meas (volume thickness)

mri_glmfit \

--y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \

--fsgd FSGD/{$study}.fsgd \

--C Contrasts/Scores_Slope.mtx\

--surf fsaverage {$hemi}\

--mask lhYeo2011_7NetworksConfidence_N1000.mgz\

--glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir

end

end

end


I get the error message:

ERROR: dimension mismatch 1 between y and mask



I've also tried to run it with the .nii file found at *MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 




Any help would be appreciated!


Haley


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Re: [Freesurfer] average thickness lobe stats

[Douglas N. Greve]

Yes, you can just average them

On 4/26/2021 3:59 AM, Agurne Sampedro Calvete wrote:


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Dear Freesurfer experts,

I am trying to obtain the average thickness of the brain lobes. I am 
particularly interested in the temporal lobe.
I have run "mri_annotation2label" (--lobeStrict) and 
"mris_anatomical_stats" commands and I have obtained the average 
thickness of the different lobes in each hemisphere. However, I am 
interested in obtaining data of both hemispheres together, that is, a 
single thickness average for example for the temporal lobe. Is there a 
way to calculate it? Could I just sum both averages from each hemisphere?


Thank you very much in advance.

Kind regards,

Agurne



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Re: [Freesurfer] Error in SAMSEG preprocessing

[Alberto Del Cerro Leon]

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After 14th interaction the terminal wrote this message:

I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-05-10 13:40:01.273046: I
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:
3292375000 Hz
2021-05-10 13:40:01.281440: I
tensorflow/compiler/xla/service/service.cc:150] XLA service 0x30013a0
executing computations on platform Host. Devices:
2021-05-10 13:40:01.281470: I
tensorflow/compiler/xla/service/service.cc:158]   StreamExecutor device
(0): , 
WARNING:tensorflow:From
/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266:
checkpoint_exists (from tensorflow.python.training.checkpoint_management)
is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
VAE lesion model loaded
2021-05-10 13:40:16.471711: W tensorflow/core/framework/allocator.cc:124]
Allocation of 171720 exceeds 10% of system memory.

I tried to improve the system memory of my virtual machine but the same
error appeared.

Any suggestions?


El vie, 7 may 2021 a las 20:59, Hoopes, Andrew ()
escribió:

> If the output directory is missing seg.mgz, then samseg failed. You’ll
> have to send us the log or some sort of information about the error for us
> to debug this.
>
>
>
> Best
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro
> Leon 
> *Date: *Friday, May 7, 2021 at 6:49 AM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Error in SAMSEG preprocessing
>
> *External Email - Use Caution*
>
> Hello, I am trying to use SAMSEG to segment white matter lesions, I ran
> the following command:
>
>
>
> run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii'
> '/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate
> --lesion --lesion-mask-pattern 0 1 --output
> '/home/neuroimage/fsl/vascular/1002/'
>
>
>
> The output files were:
>
>- cost.txt
>- priors-testing.mgz
>- samseg.talairach.lta
>- template.lta
>- template_coregistered.mgz
>- template_transforms.mat
>
> However I don't find any file with the white matter lesions segmented or a
> stat file. I would send you the terminal outputs but is too extensive.
> Would you help me?
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[Freesurfer] Register Hippocampus mask to T1.nii

[Borghi, G. (Gregorio)]

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Dear All,


Due to my study, I have been unsuccessfully trying to co-register the 
hippocampal and amygdala segmented file (obtained from segmentHA_T2.sh) to my 
T1-weighted anatomical image (.nii), so that I can use the segmented file as a 
mask for later ROI analysis. However, despite trying in several ways with 
mri_robust_register and tkregister2, I have not been able to coregister the 2 
together. Any suggestions?


Kind regards,
Greg
s1034199
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