[Freesurfer] Common space

[Alberto Del Cerro Leon]

External Email - Use Caution

Good morning, I would be interested in observing regional differences in
cortical thickness without using predefined regions. However the results
offered by FreeSurfer arrange the thickness results etc. in an individual
space which is difficult to compare between subjects before labeling. Is
there a possibility to transform the results to a common mesh (like a
template) in order to perform an exploratory analysis?
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[Freesurfer] Aparc2aseg citation

[Alberto Del Cerro Leon]

External Email - Use Caution

Hi FS team, for my line of research I have used aparc2aseg with the
--labelwm --hypo-as-wm option to obtain wm measurements from a custom atlas
of the brain lobes. However I don't know how I should cite this method as
the aparc2aseg documentation does not specify.

Thanks in advance
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[Freesurfer] WMH in aparc+aseg

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello FS team! I am using the volumetric data of WMH obtained during the
recon-all in the apar+aseg.mgz file. Where I could find the description of
the method throught it is segmented? I find the  Automated Labeling of
Neuroanatomical Structures in the Human Brain but the label WMH doesn't
figure on that.

Thanks in advance
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Re: [Freesurfer] SAMSEG

[Alberto Del Cerro Leon]

External Email - Use Caution

Thanks for the explanation!!

El vie, 12 ago 2022 a las 17:04, Koen Van Leemput ()
escribió:

> External Email - Use Caution
>
> Hi Alberto,
>
> As you already indicated, it's really a combination of an unsupervised
> clustering method with a supervised shape model, so the dichotomy between
> the two doesn't neatly apply. When I think about this type of method, I
> consider it an unsupervised technique at its core, with a bit of
> supervision to constrain the solution space.
>
> Hope this helps,
>
> Koen
>
>
> On Fri, Aug 12, 2022 at 10:51 AM Alberto Del Cerro Leon <
> bertocer...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Hello, I am reading the paper "A contrast-adaptive method for
>> simultaneous whole-brain and lesion segmentation in multiple sclerosis"
>> relative to SAMSEG method and I would like to ask you a question. Due to
>> the use of a training set in the lesion shape modeling we should consider
>> SAMSEG as a supervised or unsupervised method?
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[Freesurfer] SAMSEG

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello, I am reading the paper "A contrast-adaptive method for simultaneous
whole-brain and lesion segmentation in multiple sclerosis" relative to
SAMSEG method and I would like to ask you a question. Due to the use of a
training set in the lesion shape modeling we should consider SAMSEG as a
supervised or unsupervised method?
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[Freesurfer] Problem with labels

[Alberto Del Cerro Leon]

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Hello Freesurfer Team, I am trying to use a ROI to create a label into
fsaverage. Once I registered my ROI to the fsaverage space I performed a
mri_vol2surf and mri_cor2label to obtain a label of the ROI on the
fsaverage surface. However, this label has several holes and
irregularities. I know how to edit manually with tksurfer but, is there a
method to fill the holes and smooth the borders of the label automatically?
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[Freesurfer] Transform matrix

[Alberto Del Cerro Leon]

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Hello Freesurfer team, I did a white matter atlas from surface annot with
mri_aparc2aseg. However, when I use this atlas in comparison with the
original T1 I have observed that both images don't share the transformation
matrix. Do you know how I could I fix this issue?
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[Freesurfer] SAMSEG thresholds

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am
analyzing the vascular lessions aplying several thresholds. I would expect
that lower thresholds results in lower volumes but dont seems like that.
What is the reason?
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Re: [Freesurfer] Error in SAMSEG preprocessing

[Alberto Del Cerro Leon]

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 ()
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] Error in SAMSEG preprocessing

[Alberto Del Cerro Leon]

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] help with SAMSEG

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer team, my group is interested in using the SAMSEG tool to
evaluate white matter lesions in MCI patients. We would like to use a
personalized atlas for the measure. We suppose that we need to use the flag
--atlas but we don`t know if we need a generic atlas or we need an atlas at
each subject' spaces.

Thanks in advance for your help.
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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

To obtain de stats from mri_anatomical stats i used
*>>mris_anatomical_stats -a
/usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f*
*/usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats
-b 218 rh*
In another hand, the workflow to obatian the stats from mri_segstats was:
>>*mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask
--o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz **--annot myAAL*
*>>**mri_segstats --seg
/usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz* *--ctab
/home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum
/usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats *
*-**-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0
--brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in
/usr/local/freesurfer/subjects/218/mri/norm.mgz*
*--in-intensity-name norm --in-intensity-units MR --subject 218
--surf-wm-vol --etiv*

El lun, 5 abr 2021 a las 15:50, Douglas N. Greve ()
escribió:

> What are your command lines?
>
> On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Thanks a lot, It works!, now I have obtained values to ctx and wm volumes
> for each area. However when I look at the gray matter volume values
> calculated by mri_anatomical stats, the results are pretty similar to the
> ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In
> that case what measure will be more suitable?
>
> El lun, 29 mar 2021 a las 5:22, Douglas N. Greve ()
> escribió:
>
>> You'll need to create your own color table by adding 3000 to the left
>> hemi structures and 4000 to the right hemi structures. Look at the 3000s
>> and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>>
>> On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> Hello Douglas, i tried but when i look at the wmparc.mgz created by the
>> code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown
>> --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names
>> from FreeSurferColorLUT instead of the names in the colorLUT
>> associated with myAAL.annot then the ROIs are disorganized. Could you help
>> me with this problem?
>>
>> El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (<
>> dgr...@mgh.harvard.edu>) escribió:
>>
>>> Look in recon-all.log to find the command that creates the wmparc.mgz.
>>> Run that command changing the aparc annot to your annot and the output to a
>>> new file name. Look in wmparc.stats; at the top will be an mri_segstats
>>> command line. Copy that command line changing the file names as needed.
>>>
>>> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>>>
>>> External Email - Use Caution
>>> Thanks!, how can I obtain the white matter volume stats using my
>>> annotation file?
>>>
>>> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (<
>>> dgr...@mgh.harvard.edu>) escribió:
>>>
>>>> I think they will give very similar results, but my guess is that #1 is
>>>> a little better
>>>>
>>>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>>>
>>>> External Email - Use Caution
>>>> I want to use the annotation file created by myself in fsaverage to
>>>> calculate the anatomical stats, but i dont know what is the best workflow.
>>>>
>>>> 1. Convert the annotation file to each subject space using mri_sur2surf
>>>> and using mri_anatomical_stats in each subject
>>>> 2. Convert the surface of each subject to fsaverage space and use
>>>> mri_segstats to obtain the data, in this case i dont know what surface i
>>>> have to convert to fsaverage space to do it (i can see thickness
>>>> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
>>>> matter volume)
>>>>
>>>> Any idea?
>>>>
>>>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
>>>> escribió:
>>>>
>>>>> Hi Alberto
>>>>>
>>>>>
>>>>>
>>>>>1. And 4. Are not properties of single surfaces – they are
>>>>>computed from the white and the pial. For 2 and 3 that is really up to 
>>>>> you
>>>>>
>>>>> Cheers
>>>>> Bruce
>>>>>
>>>>>
>>>>>
>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>> 

Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

Thanks a lot, It works!, now I have obtained values to ctx and wm volumes
for each area. However when I look at the gray matter volume values
calculated by mri_anatomical stats, the results are pretty similar to the
ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In
that case what measure will be more suitable?

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve ()
escribió:

> You'll need to create your own color table by adding 3000 to the left hemi
> structures and 4000 to the right hemi structures. Look at the 3000s and
> 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>
> On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Douglas, i tried but when i look at the wmparc.mgz created by the
> code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names
> from FreeSurferColorLUT instead of the names in the colorLUT
> associated with myAAL.annot then the ROIs are disorganized. Could you help
> me with this problem?
>
> El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ()
> escribió:
>
>> Look in recon-all.log to find the command that creates the wmparc.mgz.
>> Run that command changing the aparc annot to your annot and the output to a
>> new file name. Look in wmparc.stats; at the top will be an mri_segstats
>> command line. Copy that command line changing the file names as needed.
>>
>> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> Thanks!, how can I obtain the white matter volume stats using my
>> annotation file?
>>
>> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (<
>> dgr...@mgh.harvard.edu>) escribió:
>>
>>> I think they will give very similar results, but my guess is that #1 is
>>> a little better
>>>
>>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>>
>>> External Email - Use Caution
>>> I want to use the annotation file created by myself in fsaverage to
>>> calculate the anatomical stats, but i dont know what is the best workflow.
>>>
>>> 1. Convert the annotation file to each subject space using mri_sur2surf
>>> and using mri_anatomical_stats in each subject
>>> 2. Convert the surface of each subject to fsaverage space and use
>>> mri_segstats to obtain the data, in this case i dont know what surface i
>>> have to convert to fsaverage space to do it (i can see thickness
>>> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
>>> matter volume)
>>>
>>> Any idea?
>>>
>>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
>>> escribió:
>>>
>>>> Hi Alberto
>>>>
>>>>
>>>>
>>>>1. And 4. Are not properties of single surfaces – they are computed
>>>>from the white and the pial. For 2 and 3 that is really up to you
>>>>
>>>> Cheers
>>>> Bruce
>>>>
>>>>
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del
>>>> Cerro Leon
>>>> *Sent:* Monday, March 8, 2021 7:02 AM
>>>> *To:* Freesurfer support list 
>>>> *Subject:* [Freesurfer] Problem with freesurfer measures
>>>>
>>>>
>>>>
>>>> *External Email - Use Caution*
>>>>
>>>> Hello Freesurfer team, I am using an annotation file that i've created
>>>> previously to obtain the measures of some ROIs. To do that i am using de
>>>> commands mri_surf2surf and mri_segstats. I want to obtain the following
>>>> measures:
>>>>
>>>> 1. Gray and White Matter Volume
>>>>
>>>> 2. Folding Index
>>>>
>>>> 3. Curvature measures
>>>>
>>>> 4. Thickness
>>>>
>>>> However I don't know what surface in the surf folder of each subject I
>>>> have to use. Could u help me?
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> *MailScanner has detected a possible fraud attempt from
>>>> "secure-web.cisco.com" claiming to be*
>>>> https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9QEXcl20ViD3v1z-M2EnYwrZWMYqvtsknqADt-sYTrwIi7

Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Douglas, i tried but when i look at the wmparc.mgz created by the
code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names
from FreeSurferColorLUT instead of the names in the colorLUT
associated with myAAL.annot then the ROIs are disorganized. Could you help
me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ()
escribió:

> Look in recon-all.log to find the command that creates the wmparc.mgz. Run
> that command changing the aparc annot to your annot and the output to a new
> file name. Look in wmparc.stats; at the top will be an mri_segstats command
> line. Copy that command line changing the file names as needed.
>
> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Thanks!, how can I obtain the white matter volume stats using my
> annotation file?
>
> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ()
> escribió:
>
>> I think they will give very similar results, but my guess is that #1 is a
>> little better
>>
>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> I want to use the annotation file created by myself in fsaverage to
>> calculate the anatomical stats, but i dont know what is the best workflow.
>>
>> 1. Convert the annotation file to each subject space using mri_sur2surf
>> and using mri_anatomical_stats in each subject
>> 2. Convert the surface of each subject to fsaverage space and use
>> mri_segstats to obtain the data, in this case i dont know what surface i
>> have to convert to fsaverage space to do it (i can see thickness
>> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
>> matter volume)
>>
>> Any idea?
>>
>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
>> escribió:
>>
>>> Hi Alberto
>>>
>>>
>>>
>>>1. And 4. Are not properties of single surfaces – they are computed
>>>    from the white and the pial. For 2 and 3 that is really up to you
>>>
>>> Cheers
>>> Bruce
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del
>>> Cerro Leon
>>> *Sent:* Monday, March 8, 2021 7:02 AM
>>> *To:* Freesurfer support list 
>>> *Subject:* [Freesurfer] Problem with freesurfer measures
>>>
>>>
>>>
>>> *External Email - Use Caution*
>>>
>>> Hello Freesurfer team, I am using an annotation file that i've created
>>> previously to obtain the measures of some ROIs. To do that i am using de
>>> commands mri_surf2surf and mri_segstats. I want to obtain the following
>>> measures:
>>>
>>> 1. Gray and White Matter Volume
>>>
>>> 2. Folding Index
>>>
>>> 3. Curvature measures
>>>
>>> 4. Thickness
>>>
>>> However I don't know what surface in the surf folder of each subject I
>>> have to use. Could u help me?
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

Thanks!, how can I obtain the white matter volume stats using my annotation
file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ()
escribió:

> I think they will give very similar results, but my guess is that #1 is a
> little better
>
> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> I want to use the annotation file created by myself in fsaverage to
> calculate the anatomical stats, but i dont know what is the best workflow.
>
> 1. Convert the annotation file to each subject space using mri_sur2surf
> and using mri_anatomical_stats in each subject
> 2. Convert the surface of each subject to fsaverage space and use
> mri_segstats to obtain the data, in this case i dont know what surface i
> have to convert to fsaverage space to do it (i can see thickness
> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
> matter volume)
>
> Any idea?
>
> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
> escribió:
>
>> Hi Alberto
>>
>>
>>
>>1. And 4. Are not properties of single surfaces – they are computed
>>from the white and the pial. For 2 and 3 that is really up to you
>>
>> Cheers
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro
>> Leon
>> *Sent:* Monday, March 8, 2021 7:02 AM
>> *To:* Freesurfer support list 
>> *Subject:* [Freesurfer] Problem with freesurfer measures
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hello Freesurfer team, I am using an annotation file that i've created
>> previously to obtain the measures of some ROIs. To do that i am using de
>> commands mri_surf2surf and mri_segstats. I want to obtain the following
>> measures:
>>
>> 1. Gray and White Matter Volume
>>
>> 2. Folding Index
>>
>> 3. Curvature measures
>>
>> 4. Thickness
>>
>> However I don't know what surface in the surf folder of each subject I
>> have to use. Could u help me?
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqexfnx4M_Pdm9J5uI07IHMoSLX06nTKmLoGpCM__s_0BMxj3yFWmG-DrcG6_hwmbQ4lmwutoIJ7LgzXFCY1kq67Vh2ew-rSx7g1EsGVdqylYYD-iDG_k-YXsbd2bEshDXD1Qem3t3Vtnd2vU-YadqAhVEksxzWDJrWr5lnPwyL89yQGUfLXDJIiRGxyCQZxSHNkSoSCXq9BCZ85lPb6M33BVmSYeBvf-nyCBHvN7NQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

I want to use the annotation file created by myself in fsaverage to
calculate the anatomical stats, but i dont know what is the best workflow.

1. Convert the annotation file to each subject space using mri_sur2surf and
using mri_anatomical_stats in each subject
2. Convert the surface of each subject to fsaverage space and use
mri_segstats to obtain the data, in this case i dont know what surface i
have to convert to fsaverage space to do it (i can see thickness
(lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
escribió:

> Hi Alberto
>
>
>
>1. And 4. Are not properties of single surfaces – they are computed
>from the white and the pial. For 2 and 3 that is really up to you
>
> Cheers
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro
> Leon
> *Sent:* Monday, March 8, 2021 7:02 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Problem with freesurfer measures
>
>
>
> *External Email - Use Caution*
>
> Hello Freesurfer team, I am using an annotation file that i've created
> previously to obtain the measures of some ROIs. To do that i am using de
> commands mri_surf2surf and mri_segstats. I want to obtain the following
> measures:
>
> 1. Gray and White Matter Volume
>
> 2. Folding Index
>
> 3. Curvature measures
>
> 4. Thickness
>
> However I don't know what surface in the surf folder of each subject I
> have to use. Could u help me?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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[Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer team, I am using an annotation file that i've created
previously to obtain the measures of some ROIs. To do that i am using de
commands mri_surf2surf and mri_segstats. I want to obtain the following
measures:
1. Gray and White Matter Volume
2. Folding Index
3. Curvature measures
4. Thickness
However I don't know what surface in the surf folder of each subject I have
to use. Could u help me?
___
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Re: [Freesurfer] Hippocampal segmentation

[Alberto Del Cerro Leon]

External Email - Use Caution

Then How FreeSurfer calculates the volume, curvature etc from
Hippocampus and How could I check it?

El vie, 26 feb 2021 a las 14:44, Douglas N. Greve ()
escribió:

> Hippocampus is not part of the surface
>
> On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfers, I am doing an AAL atlas on freesurfer using
> mri_vol2surf and editing the labels manually. However when I was editing
> the labels in tksurfer the hippocampal field is quite bad. I tried to look
> the segmentation used by you in labels but I didn't find it. How could I
> segment the Hippocampus
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Hippocampal segmentation

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf
and editing the labels manually. However when I was editing the labels in
tksurfer the hippocampal field is quite bad. I tried to look the
segmentation used by you in labels but I didn't find it. How could I
segment the Hippocampus
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[Freesurfer] vascular damage meassures

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer, my lab is interested in measuring the vascular damage in
different subjects. I read that Freesurfer can measure the hypointesities
characteristic of brain damage in an automated way. However I couldn't find
the properly workflow to do that

Someone could help us?
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Re: [Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

I found the vertex for the holes but how can i modify them or how can I
solve them?

El mié, 27 ene 2021 a las 16:36, Douglas N. Greve ()
escribió:

> Look at the surface superimposed on the volume along with the AAL
> segmentation to make sure that it intersects the segmentation at all
> vertices. You can find the vertex numbers for the holes, and then go
> specifically to that vertex
>
> On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfer team, I did an AAL atlas on the surface using
> mri_vol2surf, however when I look at this overlay there are many holes in
> the labels with vertices that don't belong to any label. Could u help me
> with this problem?
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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[Freesurfer] help with labels

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfer team, I did an AAL atlas on the surface using
mri_vol2surf, however when I look at this overlay there are many holes in
the labels with vertices that don't belong to any label. Could u help me
with this problem?
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[Freesurfer] Holes in my ROIs

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfers, I created surface image based on AAL with mri_vol2surf.
However i see that in some regions there are a lot of holes, i thought that
probably is for the presence of subcortical regions in the AAL.ni. There is
some workflow to select the regions from my volume to do mri_vol2sur? Can I
create another volume from my AAL.nii selecting only the surface regions?
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Re: [Freesurfer] asegstats2table {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

I employed labels based on AAL atlas (volume ROIs) but I registered them
into the surface with mri_vol2surf. So I have multiple labels on the surface

El jue, 17 dic 2020 a las 21:19, Cordero, Devani Coryn (<
dccord...@mgh.harvard.edu>) escribió:

> Hi Alberto,
>
> My name is Devani Cordero, I'm a research technician for the FreeSurfer
> lab. You can absolutely use asegstats2table. First, what kind of labels did
> you create? Did you make them based off of a volume such as T1.mgz or did
> you create them on a surface?
>
> Let me know!
>
> Devani
>
> Devani C. Cordero
>
> *Data Analyst | Intern Supervisor *
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> p: (661) 904-3534
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro
> Leon 
> *Sent:* Friday, December 11, 2020 6:57 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] asegstats2table
>
>
> External Email - Use Caution
>
> Hello Freesurfers, I have a question about the command asegstats2table. I
> want to obtain the structural data of a group set based on labels created
> by myself. I see that this is possible with mris_anatomicalstats for 1
> subject but can I obtain the data for all my subjects in some way like
> asegstats2table using my labels?
> ___
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Re: [Freesurfer] labels in the surface {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello, i used this code:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.mgh

Also i tried to map the AAL into the surface of fsaverage with:
mri_vol2surf --mov /home/neuroimage/fsl/FreeSurfer/AAL.nii --reg
/home/neuroimage/fsl/FreeSurfer/fsaverage_AAL/AAL_MNI2fsaverage.dat
--projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh_fsaverageAAL.mgh

The regions of the 2 methods are pretty similar but both have some holes
into the ROIs


El dom, 13 dic 2020 a las 18:50, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> This might be the way it is given that the AAL is volume-based and you are
> trying to put it on the surface. What is your vol2surf command?
>
> On 12/10/2020 6:59 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfer team
> With your help i obtained a AAL atlas on the surface and 1 label for each
> region. However, when I load the label into the inflate image, I obtain
> something like the one submitted in this e-mail. I expected a solid ROI on
> the surface to obtain the volume, curvature, etc of the entire region. It's
> something wrong? I am loading the label in an incorrect way?
>
> The image represent the label of the anterior cingulate into the inflated
> image
>
> ___
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>
>
> ___
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[Freesurfer] asegstats2table

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfers, I have a question about the command asegstats2table. I
want to obtain the structural data of a group set based on labels created
by myself. I see that this is possible with mris_anatomicalstats for 1
subject but can I obtain the data for all my subjects in some way like
asegstats2table using my labels?
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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

Then, now that I have the AAL in the surface I should make a label for
every region in the AAL_surface image with mri_vol2label with surf option
and run mri_label2label for every label and every subject in my study. Is
this the correct workflow?

El lun, 30 nov 2020 a las 16:26, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> Oh, don't use .img as it cannot handle the surface dimensions.
> Technically, nifti cannot either, but I hacked our nifti version to
> accommodate. Or use mgh as you have done.
>
> On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> First of all, thanks you Douglas for the support.
> As I said i run the mri_vol2surf and I obtained an error:
>
> mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
> --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
> srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
> Done loading volume
> Computing registration from header.
>   Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target
> reference.
> Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white
> Done reading source surface
> Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
>  1 0.5 0.5 0.5
> using old
> Done mapping volume to surface
> Number of source voxels hit = 104840
> Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
> Dim: 161783 1 1
> ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768
>
> However I noticed that if i use the format .guii or .mgh this error
> message doesn't appear. Could I continue with the image in this format?
> What's the difference that makes this error appear with .img format?
>
> El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> Can you send the full terminal output?
>>
>> On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> I tried to run mri_vol2surf with the following command: mri_vol2surf
>> --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac
>> 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i
>> obtain an error ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768.
>> How can i fix it?
>>
>> El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve (<
>> dgr...@mgh.harvard.edu>) escribió:
>>
>>> Which MNI space? If mni152, then run recon-all on the mni152 template,
>>> then run mri_vol2surf with --regheader  mni152subjectname; also include
>>> --projfrac 0.5. But before you do that , load the AAL atlas onto the
>>> mni152subject with the surfaces to make sure everything aligns. You might
>>> want to do this with the colin27 brain instead because I think that is what
>>> the AAL atlas is defined on.
>>>
>>> On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:
>>>
>>> External Email - Use Caution
>>> Hello everyone, I tried to follow your instruction about how to get the
>>> fresurfer stats in AAL ROIs. I have an image .nii with the labels of the
>>> AAL in the MNI space (i submit this image in the e-mail). Can I use this
>>> image in the mri_vol2surf? If so, i suppose that this image would be the
>>> input one, but i don't know what is registration file in the syntax of
>>> mri_vol2surf
>>>
>>> Sorry for the inconvenience, Alberto
>>>
>>> ___
>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>>> be* 
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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

First of all, thanks you Douglas for the support.
As I said i run the mri_vol2surf and I obtained an error:

mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target reference.
Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white
Done reading source surface
Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 104840
Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
Dim: 161783 1 1
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768

However I noticed that if i use the format .guii or .mgh this error
message doesn't appear. Could I continue with the image in this format?
What's the difference that makes this error appear with .img format?

El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> Can you send the full terminal output?
>
> On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> I tried to run mri_vol2surf with the following command: mri_vol2surf --src
> /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5
> --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i
> obtain an error ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768.
> How can i fix it?
>
> El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> Which MNI space? If mni152, then run recon-all on the mni152 template,
>> then run mri_vol2surf with --regheader  mni152subjectname; also include
>> --projfrac 0.5. But before you do that , load the AAL atlas onto the
>> mni152subject with the surfaces to make sure everything aligns. You might
>> want to do this with the colin27 brain instead because I think that is what
>> the AAL atlas is defined on.
>>
>> On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> Hello everyone, I tried to follow your instruction about how to get the
>> fresurfer stats in AAL ROIs. I have an image .nii with the labels of the
>> AAL in the MNI space (i submit this image in the e-mail). Can I use this
>> image in the mri_vol2surf? If so, i suppose that this image would be the
>> input one, but i don't know what is registration file in the syntax of
>> mri_vol2surf
>>
>> Sorry for the inconvenience, Alberto
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
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[Freesurfer] mri_vol2surf

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello, I am trying to run mri_vol2sur to obtain the AAL atlas on
freesurfer. i used this command line
"mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img"

However i received an error saying that ncols 161783 in volume exceeds
32768.

I was reading the wiki, could I avoid the error with -noreshape command?
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[Freesurfer] mri_vol2surf

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello, I have a couple of questions:

1. I asked before how to obtain AAL labels on Freesurfer. I am following
your instructions, but I don't know how to load the AAL onto my T1w
template to ensure everything aligns

2. Secondly, I tried to run mri_vol2surf with the following command:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img.
However I obtained an error "ANALYZE FORMAT ERROR: ncols 161783 in volume
exceeds 32768". How can I fix it?
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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

I tried to run mri_vol2surf with the following command: mri_vol2surf --src
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5
--hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i
obtain an error ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768.
How can i fix it?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve ()
escribió:

> Which MNI space? If mni152, then run recon-all on the mni152 template,
> then run mri_vol2surf with --regheader  mni152subjectname; also include
> --projfrac 0.5. But before you do that , load the AAL atlas onto the
> mni152subject with the surfaces to make sure everything aligns. You might
> want to do this with the colin27 brain instead because I think that is what
> the AAL atlas is defined on.
>
> On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello everyone, I tried to follow your instruction about how to get the
> fresurfer stats in AAL ROIs. I have an image .nii with the labels of the
> AAL in the MNI space (i submit this image in the e-mail). Can I use this
> image in the mri_vol2surf? If so, i suppose that this image would be the
> input one, but i don't know what is registration file in the syntax of
> mri_vol2surf
>
> Sorry for the inconvenience, Alberto
>
> ___
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>
>
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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

How can I load the AAL onto the mni152 subject with the surface?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve ()
escribió:

> Which MNI space? If mni152, then run recon-all on the mni152 template,
> then run mri_vol2surf with --regheader  mni152subjectname; also include
> --projfrac 0.5. But before you do that , load the AAL atlas onto the
> mni152subject with the surfaces to make sure everything aligns. You might
> want to do this with the colin27 brain instead because I think that is what
> the AAL atlas is defined on.
>
> On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello everyone, I tried to follow your instruction about how to get the
> fresurfer stats in AAL ROIs. I have an image .nii with the labels of the
> AAL in the MNI space (i submit this image in the e-mail). Can I use this
> image in the mri_vol2surf? If so, i suppose that this image would be the
> input one, but i don't know what is registration file in the syntax of
> mri_vol2surf
>
> Sorry for the inconvenience, Alberto
>
> ___
> Freesurfer mailing 
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>
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[Freesurfer] About mri_vol2surf

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello everyone, I tried to follow your instruction about how to get the
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the
AAL in the MNI space (i submit this image in the e-mail). Can I use this
image in the mri_vol2surf? If so, i suppose that this image would be the
input one, but i don't know what is registration file in the syntax of
mri_vol2surf

Sorry for the inconvenience, Alberto
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Re: [Freesurfer] Help with MRI labels {Disarmed}

[Alberto Del Cerro Leon]

External Email - Use Caution

I want to obtain gray matter, withe matter volume, thickness and curvature
based on AAL segmentation.

El jue., 12 nov. 2020 15:27, Douglas N. Greve 
escribió:

> So you want the AAL atlas on the surface? If so, then run recon-all on the
> AAL anatomical T1w volume template, then use mri_vol2surf to sample the
> labels on the surface, then use this surface segmentation or extract labels
> (mri_cor2label with --surf option) or convert to an annotation
> (mris_seg2annot)
>
>
> On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
> cognitive and computational neuroscience laboratory (LNCyC) at the
> biomedical technology center (CTB) of the Polytechnic University of Madrid
> (UPM). I am currently extracting the structural data from the T1 images of
> my project and I would like to extract the volume, thickness and curvature
> data in the regions of interest where I obtained results in
> electrophysiology (MEG). The point is that for this data I used the AAL
> atlas and I would like to use these regions to obtain structural data in
> FreeSurfer. Researching on the internet I have read that this is possible
> with the mri_label2vol command but I would like to know how I can proceed
> to obtain this data. Can you guide me in this process?
>
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[Freesurfer] Help with MRI labels

[Alberto Del Cerro Leon]

External Email - Use Caution

Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
cognitive and computational neuroscience laboratory (LNCyC) at the
biomedical technology center (CTB) of the Polytechnic University of Madrid
(UPM). I am currently extracting the structural data from the T1 images of
my project and I would like to extract the volume, thickness and curvature
data in the regions of interest where I obtained results in
electrophysiology (MEG). The point is that for this data I used the AAL
atlas and I would like to use these regions to obtain structural data in
FreeSurfer. Researching on the internet I have read that this is possible
with the mri_label2vol command but I would like to know how I can proceed
to obtain this data. Can you guide me in this process?
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