date:20210202

Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

2021-02-02 Thread Hoopes, Andrew

Hi Alex,

After sourcing the dev distribution, can you run:

fspython -m pip install h5py==2.10.0

This is an unfortunate bug with older versions of keras and newer versions of 
h5py, but we’ll be upgrading our internal scripts soon to deal with this. 
Thanks for point this out - I’ll put a note in the dev TF-install instructions.

As for dealing with multiple FS versions, just install them in different 
directories. Something like:

/path/to/freesurfer/6.0.0
/path/to/freesurfer/7.1.1
/path/to/freesurfer/dev
etc…

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 

Date: Tuesday, February 2, 2021 at 1:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

External Email - Use Caution
Thank you for your help!

I have tested the hypothalamus segmentation on the development version of FS, 
and this was the error output that I got (see below). How should I proceed to 
fix this?

:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2

Using 1 thread

2021-02-02 12:19:04.878273: I 
tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports 
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-02 12:19:04.899000: I 
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 
295000 Hz
2021-02-02 12:19:04.899178: I tensorflow/compiler/xla/service/service.cc:150] 
XLA service 0x20b88f0 executing computations on platform Host. Devices:
2021-02-02 12:19:04.899215: I tensorflow/compiler/xla/service/service.cc:158]   
StreamExecutor device (0): , 
processing 1/1
Traceback (most recent call last):
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 1464, in 
main()
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 91, in main
threads=args.threads
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 165, in predict
net = build_model(path_model, model_input_shape, len(label_list))
  File 
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
 line 579, in build_model
net.load_weights(model_file, by_name=True)
  File 
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py",
 line 1514, in load_weights
saving.load_weights_from_hdf5_group_by_name(f, self.layers)
  File 
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py",
 line 839, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'

Also, what's the best way for me to run a second version of Freesurfer on the 
same computer? I used a virtualbox, but is there a way to run it outside of 
that?

Thank you so much for the help and stay safe,
Alex



On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
It is not in version 7. You'll have to download a development version of FS to 
run it.
On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of 
Autism and Developmental Neuroscience wrote:

External Email - Use Caution
Dear Freesurfer experts,

I am having some trouble getting the hypothalamus segmentation recognized on 
the command line for FreeSurfer 7.1.0. Is it even available for this version? 
If not, will it work on the 6.0 or the 7.1.1 version?

Thanks and stay safe!

All the best,
Alex



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Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

2021-02-02 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Thank you for your help!

I have tested the hypothalamus segmentation on the development version of
FS, and this was the error output that I got (see below). How should I
proceed to fix this?

:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2

Using 1 thread

2021-02-02 12:19:04.878273: I
tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-02-02 12:19:04.899000: I
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:
295000 Hz
2021-02-02 12:19:04.899178: I
tensorflow/compiler/xla/service/service.cc:150] XLA service 0x20b88f0
executing computations on platform Host. Devices:
2021-02-02 12:19:04.899215: I
tensorflow/compiler/xla/service/service.cc:158]   StreamExecutor device
(0): , 
processing 1/1
Traceback (most recent call last):
  File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 1464, in 
main()
  File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 91, in main
threads=args.threads
  File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 165, in predict
net = build_model(path_model, model_input_shape, len(label_list))
  File
"/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 579, in build_model
net.load_weights(model_file, by_name=True)
  File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py",
line 1514, in load_weights
saving.load_weights_from_hdf5_group_by_name(f, self.layers)
  File
"/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py",
line 839, in load_weights_from_hdf5_group_by_name
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'

Also, what's the best way for me to run a second version of Freesurfer on
the same computer? I used a virtualbox, but is there a way to run it
outside of that?

Thank you so much for the help and stay safe,
Alex

On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve 
wrote:

> It is not in version 7. You'll have to download a development version of
> FS to run it.
>
> On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am having some trouble getting the hypothalamus segmentation recognized
> on the command line for FreeSurfer 7.1.0. Is it even available for this
> version? If not, will it work on the 6.0 or the 7.1.1 version?
>
> Thanks and stay safe!
>
> All the best,
> Alex
>
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Re: [Freesurfer] white matter volume

2021-02-02 Thread Sara Lyn

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If that's the correct way to do it then yes since I don't know about this.
If not, is the volume of white matter obtained from freesurfers glmfit
group analyses?

On Tue, Feb 2, 2021 at 11:39 AM Douglas N. Greve 
wrote:

> sorry, still don't understand. do you want to get the volume of WM from
> DTI?
>
> On 2/2/2021 11:19 AM, Sara Lyn wrote:
>
> External Email - Use Caution
> Hi Dr Greve,
>
> Instead of using DTI to get at the FA/MD etc measures is there a way to
> get at the volume of the white matter?
>
> Best,
> Sara
>
> On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve 
> wrote:
>
>> Not sure what you mean
>>
>> On 2/1/2021 12:32 PM, Sara Lyn wrote:
>>
>> External Email - Use Caution
>> Hi,
>>
>> Is there a way to get at the white matter volume from a group analysis?
>>
>> Sara
>>
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Re: [Freesurfer] white matter volume

2021-02-02 Thread Douglas N. Greve


sorry, still don't understand. do you want to get the volume of WM from DTI?

On 2/2/2021 11:19 AM, Sara Lyn wrote:


External Email - Use Caution

Hi Dr Greve,

Instead of using DTI to get at the FA/MD etc measures is there a way 
to get at the volume of the white matter?


Best,
Sara

On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Not sure what you mean

On 2/1/2021 12:32 PM, Sara Lyn wrote:


External Email - Use Caution

Hi,

Is there a way to get at the white matter volume from a group
analysis?

Sara

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Re: [Freesurfer] white matter volume

2021-02-02 Thread Sara Lyn

External Email - Use Caution

Hi Dr Greve,

Instead of using DTI to get at the FA/MD etc measures is there a way to get
at the volume of the white matter?

Best,
Sara

On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve 
wrote:

> Not sure what you mean
>
> On 2/1/2021 12:32 PM, Sara Lyn wrote:
>
> External Email - Use Caution
> Hi,
>
> Is there a way to get at the white matter volume from a group analysis?
>
> Sara
>
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Re: [Freesurfer] Failed tissue type check {Disarmed}

2021-02-02 Thread Julie Ottoy

External Email - Use Caution

Hi Doug,

I tried these fixes but they still give me the error message below. I did
replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab
in the aux folder ?

Thanks,
Julie

On Tue, 12 Jan 2021 at 10:37, Julie Ottoy  wrote:

> Hi Doug
>
> I tried that as well but getting the same error as with --replace 29 3.
>
> ERROR: CTABpruneCTab(): ctab does not have segid 2
>
>
> Thanks,
> julie
>
> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Try using --replace 29 2
>>
>>
>> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Hi Doug
>>
>> Thanks for your reply. I tried both your suggestions, but it seems as
>> though they both ran into an error.
>>
>> For your first suggestion, i.e. adding --replace 29 3 to the command line
>> of gtmpvc, I get the error:
>>
>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>>
>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>>
>> Reading 057_S_5295re/mri/gtmseg.lta
>>
>> Replacing 19
>>
>> Pruning ctab
>>
>> ERROR: CTABpruneCTab(): ctab does not have segid 3
>>
>>
>> For your second suggestion, i.e. I replaced the following line in the
>> ctab:
>>
>>   29  Left-undetermined   135 206 2350  -1
>>
>> ==> replaced by:  29  Left-undetermined   135 206 2350  3
>>
>>
>> I get the error:
>>
>> Computing Seg in input space
>>
>> Building GTM DoVoxFracCor=0
>>
>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>>
>> It may be that there are no voxels for this seg when mapped into the
>> input space.
>>
>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
>> registration
>>
>>  Build time 5.9690, err = 1
>>
>>
>> Thank you,
>>
>> Julie
>>
>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> You can use the fix from my previous email or you can add the following
>>> line any were into the gtmseg.ctab file:
>>>  29  Left-undetermined   135 206 235 0 3
>>>
>>>
>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>>
>>> External Email - Use Caution
>>> Sorry I would like to correct my previous post. The subject also failed
>>> with PVC.
>>> I see now that the issue is happening during the gtm seg stage where it
>>> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
>>> set.
>>> For your information: I ran the standard FS and petsurfer pipeline as
>>> outlined on the wiki. I tried two gtm seg commands:
>>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
>>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
>>> --subseg-cblum-wm
>>>
>>> Thank you for your help,
>>> Julie
>>>
>>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
>>> wrote:
>>>
 External Email - Use Caution
 Dear Doug,

 I have the same issue as the people below. I was wondering if this was
 solved in the meantime.

 I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC
 and got the following error in only one of my subjects. When I ran the same
 subject with PVC and specified psf, it did run fine.

 $Id: mri_gtmpvc.c,-
 setenv -
 cd -
 mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
 gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
 /gtmnopvc.output.ceregrey --rescale 8 47
 sysname  Linux
 hostname -
 machine  -
 user -
 vgthresh   0.001000
 nReplace   18
 0. 0. 0. 0. 0. 0.
 24 avail.processors, using 1
 Creating output directory /gtmnopvc.output.ceregrey
 Loading seg for gtm /ID/mri/gtmseg.mgz
 Loading seg ctab /ID/mri/gtmseg.ctab
 Reading /ID/mri/gtmseg.lta
 Replacing 18
 Pruning ctab
 Checking tissue type
 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined
 not set
 Failed tissue type check

 Any suggestions would be appreciated!
 Thank you,
 Julie

 Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
 
 2017-11-25

Re: [Freesurfer] Fwd: label to surface

2021-02-02 Thread Douglas N. Greve

I've never done it in FS, but you might be able to do it with 
mris_convert using -c option and specifying a gifti as an output


On 2/1/2021 8:19 PM, Sam W wrote:


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Hi!
Just pinging. Is there a way to get the surface+overlay file as 
mentioned above using freesurfer? Thank you!

Best regards,
Sam


-- Forwarded message -
From: *Sam W* mailto:samf...@gmail.com>>
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label to surface
To: Freesurfer support list >



Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However 
probtrackx requires a file that contains both the whole surface file 
(eg, lh.pial) as well as the overlay (the scalar values associated 
with the vertices of the roi).
I can create such a file with FSL's label2surf command which creates a 
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running 
probtrackx with the overlay from mri_label2label --outmask does not 
work. It also needs the associated pial or white surface.

Best regards,
Sam


On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


what do you mean merge with the pial?

On 7/9/2020 8:07 PM, Sam W wrote:


External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay
with mri_label2label using --outmask as you suggested, but now
I'd like to merge that overlay with the pial surface (lh.pial).
Is there a tool I can use to achieve that result?
Best regards,
Sam


On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:


External Email - Use Caution

Hi,
Is there a way to convert a label file into a
surface/overlay? Thank you!
Best regards,
Sam

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Re: [Freesurfer] White matter parcellation

2021-02-02 Thread Douglas N. Greve

The subcortical GM structures are obtained from the whole brain 
segmentation (Fischl, Neuron, 2002). The segmentation of the WM is 
performed by taking the label of the closest point on cortex (Salat, 
Neuroimage, 2009)





On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I need help trying to understand how the white matter gets 
parcellated. I have a clinical dataset, which means that the 
resolution is not as research images, but it ran without a problem. I 
would like to measure the volume of the basal ganglia and looking at 
wmparc.mgz I am not sure how Freesurfer decides where a structure ends 
and the other one begins. I am attaching two images to show what I mean.


I would really appreciate some clarification. I am using FreeSurfer 7.1.1

Thanks in advance.
José




Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
Rechts; Gerichtsstand: Hamburg | *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* www.uke.de 

Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim 
Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel




SAVE PAPER - THINK BEFORE PRINTING


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Re: [Freesurfer] cortical thickness ROI

2021-02-02 Thread Douglas N. Greve

Yes, you can use mris_apply_reg to map the label/annotation back to the 
individual, then mri_label2vol to map it into the DTI space, then use 
mri_segstats to extract the mean value from the ROI


On 2/1/2021 1:15 PM, Sara Lyn wrote:


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Hi Freesurfer developers,

I wanted to know if I could use an ROI obtained from cortical 
thickness group analysis to obtain FA values from that same ROI for 
each of the subjects. Appreciate any guidance, thank you.


Sincerely,
Sara

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Re: [Freesurfer] white matter volume

2021-02-02 Thread Douglas N. Greve


Not sure what you mean

On 2/1/2021 12:32 PM, Sara Lyn wrote:


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Hi,

Is there a way to get at the white matter volume from a group analysis?

Sara

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Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

Re: [Freesurfer] white matter volume

Re: [Freesurfer] white matter volume

Re: [Freesurfer] white matter volume

Re: [Freesurfer] Failed tissue type check {Disarmed}

Re: [Freesurfer] Fwd: label to surface

Re: [Freesurfer] White matter parcellation

Re: [Freesurfer] cortical thickness ROI

Re: [Freesurfer] white matter volume

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