[Freesurfer] mri_glmfit

[James Brown]

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Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to
run mri_glmfit between two groups using the flag "--label" to restrict
analysis within lobes.

I ran these commands on fsaverage

mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes
mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes

This created annotation files within the "labels"  folder of fsaverage,
then I ran mri_glmfit using the flag --label lh.lobes from fsaverage

I got this error message
mri_glmfit: could not scan # of lines from label file

I am ot sure what I am doing wrong. Thanks for guidance

James
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Re: [Freesurfer] questions about mri_glmfit

[James Brown]

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Dear Dr Greve, thank you so much for answers to my questions.
Regarding question 2, yes I meant leaving only columns I need, for instance
I am interested in lobes. I ran these commands on my data

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]

then mri_segstats and I got the final stats file which contain data for the
lobes rois

3201wm-lh-frontal-lobe
3203wm-lh-cingulate-lobe
3204wm-lh-occiptal-lobe
3205wm-lh-temporal-lobe
3206wm-lh-parietal-lobe
3207wm-lh-insula-lobe

4201wm-rh-frontal-lobe
4203wm-rh-cingulate-lobe
4204wm-rh-occiptal-lobe
4205wm-rh-temporal-lobe
4206wm-rh-parietal-lobe
4207wm-rh-insula-lobe


My question is can I revise the spreadsheet from the output of
aparcstats2table or asegstats2table to keep the lobar ROIs above (8
columns) then feed that data to mri_glmfit?

On 12/20/2022 12:22 PM, James Brown wrote:

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.

You can create a mask or label and feed it into mri_glmfit with --mask or
--label

2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Remove the columns you don't want?

On Tue, Dec 20, 2022 at 12:22 PM James Brown  wrote:

> Dear Freesurfer experts,
> I have 2 questions about the command mri_glmfit and I appreciate your help.
> 1- Are there any settings or flags that can be used in mri_glmfit to
> restrict statistical comparison of surface based analysis to specific ROIs
> rather than whole brain analysis. I would like to show the difference on
> the brain surface in lobes rather than in sub lobar labels.
> 2- I understand that the flag "--table" in command mri_glmfit allows for
> feeding spreadsheets instead of images. Can we restrict the number of
> columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
> occipital and parietal) left and right? Also, is there any way to generate
> a statistical map from the spreadsheet statistics?
>
> Thank you and happy holidays :)
> James
>
>
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[Freesurfer] questions about mri_glmfit

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.
2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Thank you and happy holidays :)
James
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[Freesurfer] cortical thickness in frontal lobe

[James Brown]

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Dear Freesurfer experts,
We are new to Freesurfer. We appreciate your help & apologize if the
question is simple.
We need cortical thickness in lobes instead of parcellates. Is it correct
to take the average of the parcelates from the aparc+aseg.stats file under
subjid/stats folder. For example,
cortical thickness of frontal lobe = sum of frontal parcellates  divided by
number of parcallates .
Do we need to do any correction such as weighing the surface area
measurements ?

Thank you
James
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[Freesurfer] Fwd: average lobar cortical thickness

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
(i.e. output of recon-all). I need average cortical thickness in frontal,
parietal, temporal, cingulate and occipital lobes. Is it correct to average
thickness measurement of every sub lobe roi (e.g. average thickness in
frontal lobe = average of:

   - Superior Frontal
   - Rostral and Caudal Middle Frontal
   - Pars Opercularis, Pars Triangularis, and Pars Orbitalis
   - Lateral and Medial Orbitofrontal
   - Precentral
   - Paracentral
   - Frontal Pole

and so on for other lobes...

Do we need to correct for the number of vertices in every region when we
measure the lobar average thickness?

Alternatively, do I need to run these commands to generate lobes then
measure thickness in every lobe?

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]


Thank you
James
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[Freesurfer] average lobar cortical thickness

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
(i.e. output of recon-all). I need average cortical thickness in frontal,
parietal, temporal, cingulate and occipital lobes. Is it correct to average
thickness measurement of every sub lobe roi (e.g. average thickness in
frontal lobe = average of:

   - Superior Frontal
   - Rostral and Caudal Middle Frontal
   - Pars Opercularis, Pars Triangularis, and Pars Orbitalis
   - Lateral and Medial Orbitofrontal
   - Precentral
   - Paracentral
   - Frontal Pole

and so on for other lobes...

Do we need to correct for the number of vertices in every region when we
measure the lobar average thickness?

Alternatively, do I need to run these commands to generate lobes then
measure thickness in every lobe?

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]


Thank you
James
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 .
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Re: [Freesurfer] mri_segment

[James Brown]

External Email - Use Caution

Dear Dr Bruce, Fischl,
Indeed, the input to mri_segment is "brain.mgz", when I run mri_cnr on
brain.mgz I see
white = 102.3+-6.1, gray = 74.8+-16.7, csf = 51.5+-17.1

WM intensity is around 110  . I didn't know that intensity normalization
takes two steps! Thank you for pointing this out.


I would check your results to see if it is doing the right thing. I also
think that the input to mri_segment is not the norm.mgz, but rather the
brain.mgz, which is more aggressively normalized

On Mon, Oct 24, 2022 at 2:01 PM James Brown  wrote:

> Dear Dr Bruce, Fischl,
>
>
>
> The command was:
>
> mri_cnr $SUBJECTS_DIR/subjID/surf  $SUBJECTS_DIR/subjID/mri/norm.mgz
>
> I would like to understand the highest limit of WM intensity in a
> normalized image. I am a little bit confused about that. For instance, the
> command “mri_normlaize” puts white matter intensity around 110. It seems
> there is a high limit threshold for white matter (i.e. mri_segment puts wm
> high limit at 125 but in the manuscript I referenced it seems to be 140).
> If the image is showing higher intensity values due to a noise is it
> correct procedure to increase the high limit of WM up to 125 or 140?
>
>
> On Mon, Oct 24, 2022 at 1:46 PM James Brown  wrote:
>
>> Dear Dr Bruce, Fischl,
>>
>> Thank you very much for the detailed explanation. I would like to ask two
>> additional questions and I highly appreciate your input.
>>
>>
>>
>> -  The output of “mri_normalize” on a T1 image is something like:
>>
>>
>>
>> 3d normalization pass 1 of 2
>>
>> white matter peak found at 110
>>
>> white matter peak found at 109
>>
>> gm peak at 71 (71), valley at 38 (38)
>>
>> csf peak at 36, setting threshold to 59
>>
>> building Voronoi diagram...
>>
>>
>>
>> In this manuscript 
>> https://secure-web.cisco.com/1EhsES1ZezvIMDMxuS_URulqoaO_a1ha4QdRkq190T-vG90Ak4cg_CraqmjR8CUOtYb254N4k6pFa3b6Qi5g-MNzrqgnkFgGfoYbtwlO3XZmL_bi5ozDGEZmc_TyJbEG0wCGHLWBJPHxKZYlq26C29235IYTfatsx9a5WrZ_qtUO9G9OKnbzMqB0WVrBzE-E8kLexr19DdvYkXM1yoSuksq8Ufh2okemFrcBrQo-5gu4_A0zps-zNf4XVU0eX1irMeY_P9Ym0CIVRAIjRBCbokooOaR1abOR01Atpz12p-u3A93wtsK1OHbY-nPx4qQ27OO-iEIMCGDLagFJdmelJ5w/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F9931268%2F
>>  three
>> intensity-based contrasts WM_low (90), WM_high (140 and Gray_high (100)
>> were defined. I understand that the command “mri_normalzie” reports the
>> peak intensity of WM, GM and CSF but the highest limit of WM in any
>> “norm.mgz” is 140 by default. Is this correct?
>>
>>
>>
>> -  The output of the command “mri_cnr” is something like this:
>>
>> white = 86.5+-22.1, gray = 77.6+-29.0, csf = 66.8+-35.2
>>
>> lh CNR = 0.058
>>
>>
>>
>> Does this mean that the mean white matter intensity in the left
>> hemisphere is 86.5 and the standard deviation is 22.1? In this example, can
>> we say that the highest limit of white matter intensity in the image is 108?
>>
>>
>>
>> I apologize for asking too many questions. I appreciate the opportunity
>> to learn.
>>
>> Sincerely,
>>
>> James
>>
>>
>>
>>
>>
>> Hi James
>>
>>
>>
>> It really depends on your sequence. Some sequences, like mprage, trade
>> off SNR for CNR, so the distance between gray and white is larger, but the
>> noise in each is also larger. In that case white might end up brighter
>> because of the noise. There are also inflow effects where you get
>> non-inverted spins coming in through arteries that are very bright in
>> mprage, that you won’t see in a flash scan. We don’t actually set the gm
>> peak, just scale the white to 110-ish, then gray lands wherever the
>> intrinsic contrast of the image puts it
>>
>>
>>
>> Cheers
>>
>> Bruce
>>
>> On Sat, Oct 22, 2022 at 10:18 PM James Brown  wrote:
>>
>>> Dear Freesurfer experts,
>>> I would like to inquire about the flags "-whi" and "-ghi" in the
>>> command "mri_segement".
>>> According to FS wiki, the command "mri_normalize" sets white matter
>>> voxels around ~110 and gray matter around ~70.
>>> - The default white matter high limit in the command mri_segemnt is 125,
>>> what is the highest value to consider white matter voxels in an image? Is
>>> it 125?
>>> - What are the situations where we need to set the gray and white matter
>>> voxels at a high limit of 100 and 125 respectively in the command
>>> 

Re: [Freesurfer] mri_segment

[James Brown]

External Email - Use Caution

Dear Dr Bruce, Fischl,



The command was:

mri_cnr $SUBJECTS_DIR/subjID/surf  $SUBJECTS_DIR/subjID/mri/norm.mgz

I would like to understand the highest limit of WM intensity in a
normalized image. I am a little bit confused about that. For instance, the
command “mri_normlaize” puts white matter intensity around 110. It seems
there is a high limit threshold for white matter (i.e. mri_segment puts wm
high limit at 125 but in the manuscript I referenced it seems to be 140).
If the image is showing higher intensity values due to a noise is it
correct procedure to increase the high limit of WM up to 125 or 140?


On Mon, Oct 24, 2022 at 1:46 PM James Brown  wrote:

> Dear Dr Bruce, Fischl,
>
> Thank you very much for the detailed explanation. I would like to ask two
> additional questions and I highly appreciate your input.
>
>
>
> -  The output of “mri_normalize” on a T1 image is something like:
>
>
>
> 3d normalization pass 1 of 2
>
> white matter peak found at 110
>
> white matter peak found at 109
>
> gm peak at 71 (71), valley at 38 (38)
>
> csf peak at 36, setting threshold to 59
>
> building Voronoi diagram...
>
>
>
> In this manuscript 
> https://secure-web.cisco.com/1kLafUZhzq_EhLTyLNQ1MxMPAmSGjY2jbMGnlh44uboBMu_zOP6sk35jSHkP8jY8Mc1JqpvqVCVC7oDaL_sOyhs5CHJkpF2PfUpDKJhvuELYBXud52otlISM86vzcYW2WEdllqfOkQx14XBFpGxuR5RwbTnlZ85xTlcgBWb-0FqjXSXG9VoG2rsCUokxcFnHfIjpYsrtDEkZ6XF7iquX0ckfjAD942Y3jgqPhC6TRyn4eFnwq1LisR2V-AHffxnWOlA8IxYAuur7z8BnZGE5_M5iUfzxr6Wefl16qYJvZDSCSzDGUS_2eY7m4oYvbLgFnjV9r4K1fAWOTBMgllQvrdw/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F9931268%2F
>  three
> intensity-based contrasts WM_low (90), WM_high (140 and Gray_high (100)
> were defined. I understand that the command “mri_normalzie” reports the
> peak intensity of WM, GM and CSF but the highest limit of WM in any
> “norm.mgz” is 140 by default. Is this correct?
>
>
>
> -  The output of the command “mri_cnr” is something like this:
>
> white = 86.5+-22.1, gray = 77.6+-29.0, csf = 66.8+-35.2
>
> lh CNR = 0.058
>
>
>
> Does this mean that the mean white matter intensity in the left hemisphere
> is 86.5 and the standard deviation is 22.1? In this example, can we say
> that the highest limit of white matter intensity in the image is 108?
>
>
>
> I apologize for asking too many questions. I appreciate the opportunity to
> learn.
>
> Sincerely,
>
> James
>
>
>
>
>
> Hi James
>
>
>
> It really depends on your sequence. Some sequences, like mprage, trade off
> SNR for CNR, so the distance between gray and white is larger, but the
> noise in each is also larger. In that case white might end up brighter
> because of the noise. There are also inflow effects where you get
> non-inverted spins coming in through arteries that are very bright in
> mprage, that you won’t see in a flash scan. We don’t actually set the gm
> peak, just scale the white to 110-ish, then gray lands wherever the
> intrinsic contrast of the image puts it
>
>
>
> Cheers
>
> Bruce
>
> On Sat, Oct 22, 2022 at 10:18 PM James Brown  wrote:
>
>> Dear Freesurfer experts,
>> I would like to inquire about the flags "-whi" and "-ghi" in the command
>> "mri_segement".
>> According to FS wiki, the command "mri_normalize" sets white matter
>> voxels around ~110 and gray matter around ~70.
>> - The default white matter high limit in the command mri_segemnt is 125,
>> what is the highest value to consider white matter voxels in an image? Is
>> it 125?
>> - What are the situations where we need to set the gray and white matter
>> voxels at a high limit of 100 and 125 respectively in the command
>> mri_segment? Does the brightness of the image or motion play a role in the
>> decision of choosing high limits values?
>>
>>
>> Thank you,
>> James
>>
>
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contains patient information, please contact the Mass General Brigham 
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Re: [Freesurfer] mri_segment

[James Brown]

External Email - Use Caution

Dear Dr Bruce, Fischl,

Thank you very much for the detailed explanation. I would like to ask two
additional questions and I highly appreciate your input.



-  The output of “mri_normalize” on a T1 image is something like:



3d normalization pass 1 of 2

white matter peak found at 110

white matter peak found at 109

gm peak at 71 (71), valley at 38 (38)

csf peak at 36, setting threshold to 59

building Voronoi diagram...



In this manuscript 
https://secure-web.cisco.com/1sJwe_Z3H8ctyteSDndmgRa0Ulf0sp7KGqwyHsKQ37WNo3_OibqswecVVwiHErJG4z2hZP_5sY7eb0pCKPGBLGPBsc5B6NzrJ_A016Fxef5ipkg23QZv4iWmOXZmeAHXwH_P12s-r_odrdLUskh6P0hkFx_9u6QrxFUd82xfnFV4SWecxrWJ94i6ZTen56P_sMyKYrC4qkaGX-OAG9ulSy8Wbq-pIVXJtBBVnWBdp0Zfkafhk4BlJLfQWbPr42oH6_LtwL-oxJlLyAAW7ZtifyjqTQyIm9DtajAcUv9ctZakiGaS8U_esSA4R59k5xs-2vhmaoQ00AGMQBe6H4COauA/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F9931268%2F
 three
intensity-based contrasts WM_low (90), WM_high (140 and Gray_high (100)
were defined. I understand that the command “mri_normalzie” reports the
peak intensity of WM, GM and CSF but the highest limit of WM in any
“norm.mgz” is 140 by default. Is this correct?



-  The output of the command “mri_cnr” is something like this:

white = 86.5+-22.1, gray = 77.6+-29.0, csf = 66.8+-35.2

lh CNR = 0.058



Does this mean that the mean white matter intensity in the left hemisphere
is 86.5 and the standard deviation is 22.1? In this example, can we say
that the highest limit of white matter intensity in the image is 108?



I apologize for asking too many questions. I appreciate the opportunity to
learn.

Sincerely,

James





Hi James



It really depends on your sequence. Some sequences, like mprage, trade off
SNR for CNR, so the distance between gray and white is larger, but the
noise in each is also larger. In that case white might end up brighter
because of the noise. There are also inflow effects where you get
non-inverted spins coming in through arteries that are very bright in
mprage, that you won’t see in a flash scan. We don’t actually set the gm
peak, just scale the white to 110-ish, then gray lands wherever the
intrinsic contrast of the image puts it



Cheers

Bruce

On Sat, Oct 22, 2022 at 10:18 PM James Brown  wrote:

> Dear Freesurfer experts,
> I would like to inquire about the flags "-whi" and "-ghi" in the command
> "mri_segement".
> According to FS wiki, the command "mri_normalize" sets white matter
> voxels around ~110 and gray matter around ~70.
> - The default white matter high limit in the command mri_segemnt is 125,
> what is the highest value to consider white matter voxels in an image? Is
> it 125?
> - What are the situations where we need to set the gray and white matter
> voxels at a high limit of 100 and 125 respectively in the command
> mri_segment? Does the brightness of the image or motion play a role in the
> decision of choosing high limits values?
>
>
> Thank you,
> James
>
___
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contains patient information, please contact the Mass General Brigham 
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[Freesurfer] mri_segment

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
I would like to inquire about the flags "-whi" and "-ghi" in the command
"mri_segement".
According to FS wiki, the command "mri_normalize" sets white matter voxels
around ~110 and gray matter around ~70.
- The default white matter high limit in the command mri_segemnt is 125,
what is the highest value to consider white matter voxels in an image? Is
it 125?
- What are the situations where we need to set the gray and white matter
voxels at a high limit of 100 and 125 respectively in the command
mri_segment? Does the brightness of the image or motion play a role in the
decision of choosing high limits values?


Thank you,
James
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[Freesurfer] Creating a lobar atlas

[James Brown]

External Email - Use Caution

Dear colleagues Freesurfer experts,

I would like to create an atlas (my atlas) for the white matter like
"wmparc.mgz" so I can generate statistics.

I would like this atlas to be limited to the following structures (frontal
lobe, parietal lobe, occipital lobe and temporal lobe). I reviewed
Freesurfer tutorials  and Q in Freesurfer forum then ran the following
commands:

mri_annotation2label --subject subject --hemi lh --lobesStrict lobes

mri_annotation2label --subject subject --hemi rh --lobesStrict lobes

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask
--o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz --annot lobes --base-offset 200

Then,

mris_ca-train -t ./color.tab lh ../surf/lh.sphere.reg
../label/lh.lobes.annot SUBJECT_TEST lh.my_atlas.gcs

mris_ca-train -t ./color.tab rh ../surf/rh.sphere.reg
../label/rh.lobes.annot SUBJECT_TEST rh.my_atlas.gcs

I would like to use mri_segstats with “my atlas” to generate statistics in
lobes not in parcellates.  How can I convert lh.my_atlas.gcs and
rh.my_atlas.gcs to myatlas.mgz ?



 Thanks for your help

James
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Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Dr Bruce,
Thank you very much for answering my questions and for help. We highly
appreciate you.

All the best
James

   1. Sigma is the smoothing kernel applied to the bias field so you can
   make it pretty large depending on how high frequency your bias field is
   (typically defined by the size of your receive coils)
   2. min_dist specifies the minimum distance from the surface a voxel must
   be for it to be considered as a potential control point
   3. I don’t see why not although I’ve never tried it. It won’t fix
   slice-specific artifacts in e.g. interlaced acquisitions
   4. We estimate the bias field from the white matter, then apply it to
   the whole brain.



I don’t think nonmax_suppress will do anything without surfaces though



Cheers

Bruce

On Tue, Sep 27, 2022 at 7:20 AM James Brown  wrote:

> Dear Dr Greeve and Dr Fiscle,
> I am grateful to you guiding me through this. Indeed, I can see in
> recon-all.log how Freesurfer 7.3.2 is normalizing the Flair images. *it
> uses the command below:*
>
>  aseg.presurf.mgz -surface lh.white identity.nofile -surface rh.white
> identity.nofile FLAIR.prenorm.mgz FLAIR.norm.mgz >
>
> I tried to run the previous command without the flag -surface" and it
> seems to be working. using this command
>
>  --no-skull >
>
> I would like to inquire about the following points and I highly appreciate
> any clarification you might provide:
> 1- It seems mri_normalize uses default sigma of 8 for normalizing T1
> images and 0.5 for Flair. How far can we go up with this value? More
> specifically, when I have noticed when I increase sigma in noisy flair
> images in my dataset, I get better out put images in terms of less
> noticeable motion artifacts. Is there any cut off value for sigma? Can I
> use high values up to (e.g. 25)?
> 2-  What does the flag "-min_dist" do? I tried to find information in
> mri_normalize man (i.e. help ) but I couldn't find information about this
> flag. I assume it has to do with the flag surface and they both should be
> used together?
> 3- Can I use mri_normalize on 2D flair images ?
> 4- Is it recommended to do whole brain normalization (white/gray and csf)
> or just white matter normalization within a mask.
>
> Thank you very much for all that you do.
>
> James
>
>
>
>
>
> it looks like you are using v6. In v6, the flair might not have been
> normalized
> 
> On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote:
>
> I think you need to add something like -FLAIRpial or -T2pial so it uses it
> (in which case it will first normalize it), but hopefully someone else can
> confirm
>
> cheers
> Bruce
>
>
> On Fri, Sep 23, 2022 at 2:40 PM James Brown  wrote:
>
>> Dear Dr Bruce,
>> Thank you very much for your guidance.
>> I ran recon-all on a subject "test" using Freesurfer V6.0 and the
>> following command line is reported in the "recon-all.log":
>>
>> /usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
>> FLAIR.nii.gz -s test
>>
>> When I search for normalization of flair, I only find how Freesurfer
>> normalized T1.
>> I searched for "nonmax_suppress" and it is not in the log file. I am just
>> wondering what I am doing wrong. Thanks again for any highlights about the
>> correct method to normalize FLAIR
>>
>> Sincerely,
>>
>>
>>
>> Hi JamesB
>>
>> there is T2/FLAIR normalization in recon-all if you process it through
>> there. You can look for "nonmax_suppress" if you want to find the command
>> line
>>
>> cheers
>> Bruce
>>
>> On Fri, Sep 23, 2022 at 2:06 PM James Brown  wrote:
>>
>>> Dear Freesurfer experts,
>>> We appreciate any advice or guidance from your community of
>>> professionals and experts in the field about the issue below.
>>>
>>> Thank you for your kindness.
>>>
>>> Dear Freesurfer experts,
>>> In order to normalize white matter intensity of T1 images and correct
>>> for bias field. We do the following steps:
>>> mri_convert T1.nii.gz T1.mgz
>>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>>
>>> We would like to apply bias field correction on FLAIR images then
>>> normalize white matter intensity.
>>> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>>> Reviewing documents about N4biasfieldcorrection we realize that the
>>> algorithm has been developed to correct bias field

Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Dr Greeve and Dr Fiscle,
I am grateful to you guiding me through this. Indeed, I can see in
recon-all.log how Freesurfer 7.3.2 is normalizing the Flair images. *it
uses the command below:*



I tried to run the previous command without the flag -surface" and it seems
to be working. using this command



I would like to inquire about the following points and I highly appreciate
any clarification you might provide:
1- It seems mri_normalize uses default sigma of 8 for normalizing T1 images
and 0.5 for Flair. How far can we go up with this value? More specifically,
when I have noticed when I increase sigma in noisy flair images in my
dataset, I get better out put images in terms of less noticeable motion
artifacts. Is there any cut off value for sigma? Can I use high values up
to (e.g. 25)?
2-  What does the flag "-min_dist" do? I tried to find information in
mri_normalize man (i.e. help ) but I couldn't find information about this
flag. I assume it has to do with the flag surface and they both should be
used together?
3- Can I use mri_normalize on 2D flair images ?
4- Is it recommended to do whole brain normalization (white/gray and csf)
or just white matter normalization within a mask.

Thank you very much for all that you do.

James





it looks like you are using v6. In v6, the flair might not have been
normalized

On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote:

I think you need to add something like -FLAIRpial or -T2pial so it uses it
(in which case it will first normalize it), but hopefully someone else can
confirm

cheers
Bruce


On Fri, Sep 23, 2022 at 2:40 PM James Brown  wrote:

> Dear Dr Bruce,
> Thank you very much for your guidance.
> I ran recon-all on a subject "test" using Freesurfer V6.0 and the
> following command line is reported in the "recon-all.log":
>
> /usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
> FLAIR.nii.gz -s test
>
> When I search for normalization of flair, I only find how Freesurfer
> normalized T1.
> I searched for "nonmax_suppress" and it is not in the log file. I am just
> wondering what I am doing wrong. Thanks again for any highlights about the
> correct method to normalize FLAIR
>
> Sincerely,
>
>
>
> Hi JamesB
>
> there is T2/FLAIR normalization in recon-all if you process it through
> there. You can look for "nonmax_suppress" if you want to find the command
> line
>
> cheers
> Bruce
>
> On Fri, Sep 23, 2022 at 2:06 PM James Brown  wrote:
>
>> Dear Freesurfer experts,
>> We appreciate any advice or guidance from your community of professionals
>> and experts in the field about the issue below.
>>
>> Thank you for your kindness.
>>
>> Dear Freesurfer experts,
>> In order to normalize white matter intensity of T1 images and correct for
>> bias field. We do the following steps:
>> mri_convert T1.nii.gz T1.mgz
>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>
>> We would like to apply bias field correction on FLAIR images then
>> normalize white matter intensity.
>> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>> Reviewing documents about N4biasfieldcorrection we realize that the
>> algorithm has been developed to correct bias field correction in T1 not
>> clear if it works on FLAIR images.
>>
>> Are the steps above valid for normalizing FLAIR images or can it only be
>> applied on T1 images? I would like to send a "recon-all.log" file that
>> includes the processing steps of FLAIR. Is there any link I can use to
>> upload the file. It gets rejected every time I send it due to size
>> limitations.
>>
>> We appreciate any feedback about the proper way to correct FLAIR images
>> for bias fields and normalize white matter intensity in FLAIR images.
>>
>> Thank you
>> JamesB
>>
>> On Wed, Sep 21, 2022 at 10:18 AM James Brown  wrote:
>>
>>> Dear Freesurfer experts,
>>> In order to normalize white matter intensity of T1 images and correct
>>> for bias field. We do the following steps:
>>> mri_convert T1.nii.gz T1.mgz
>>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>>
>>> We would like to apply bias field correction on FLAIR images then
>>> normalize white matter intensity.
>>> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>>> Reviewing documents about N4biasfieldcorrection we realize that the
>

Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following
command line is reported in the "recon-all.log":

/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
FLAIR.nii.gz -s test

When I search for normalization of flair, I only find how Freesurfer
normalized T1.
I searched for "nonmax_suppress" and it is not in the log file. I am just
wondering what I am doing wrong. Thanks again for any highlights about the
correct method to normalize FLAIR

Sincerely,



Hi JamesB

there is T2/FLAIR normalization in recon-all if you process it through
there. You can look for "nonmax_suppress" if you want to find the command
line

cheers
Bruce

On Fri, Sep 23, 2022 at 2:06 PM James Brown  wrote:

> Dear Freesurfer experts,
> We appreciate any advice or guidance from your community of professionals
> and experts in the field about the issue below.
>
> Thank you for your kindness.
>
> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. We do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> We would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection we realize that the
> algorithm has been developed to correct bias field correction in T1 not
> clear if it works on FLAIR images.
>
> Are the steps above valid for normalizing FLAIR images or can it only be
> applied on T1 images? I would like to send a "recon-all.log" file that
> includes the processing steps of FLAIR. Is there any link I can use to
> upload the file. It gets rejected every time I send it due to size
> limitations.
>
> We appreciate any feedback about the proper way to correct FLAIR images
> for bias fields and normalize white matter intensity in FLAIR images.
>
> Thank you
> JamesB
>
> On Wed, Sep 21, 2022 at 10:18 AM James Brown  wrote:
>
>> Dear Freesurfer experts,
>> In order to normalize white matter intensity of T1 images and correct for
>> bias field. We do the following steps:
>> mri_convert T1.nii.gz T1.mgz
>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>
>> We would like to apply bias field correction on FLAIR images then
>> normalize white matter intensity.
>> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>> Reviewing documents about N4biasfieldcorrection we realize that the
>> algorithm has been developed to correct bias field correction in T1 not
>> clear if it works on FLAIR images.
>>
>> Are the steps above valid for normalizing FLAIR images or can it only be
>> applied on T1 images? I would like to send a "recon-all.log" file that
>> includes the processing steps of FLAIR. Is there any link I can use to
>> upload the file. It gets rejected every time I send it due to size
>> limitations.
>>
>> We appreciate any feedback about the proper way to correct FLAIR images
>> for bias fields and normalize white matter intensity in FLAIR images.
>>
>> Thank you
>> JamesB
>>
>
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals
and experts in the field about the issue below.

Thank you for your kindness.

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then
normalize white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the
algorithm has been developed to correct bias field correction in T1 not
clear if it works on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that
includes the processing steps of FLAIR. Is there any link I can use to
upload the file. It gets rejected every time I send it due to size
limitations.

We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB

On Wed, Sep 21, 2022 at 10:18 AM James Brown  wrote:

> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. We do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> We would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection we realize that the
> algorithm has been developed to correct bias field correction in T1 not
> clear if it works on FLAIR images.
>
> Are the steps above valid for normalizing FLAIR images or can it only be
> applied on T1 images? I would like to send a "recon-all.log" file that
> includes the processing steps of FLAIR. Is there any link I can use to
> upload the file. It gets rejected every time I send it due to size
> limitations.
>
> We appreciate any feedback about the proper way to correct FLAIR images
> for bias fields and normalize white matter intensity in FLAIR images.
>
> Thank you
> JamesB
>
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. We do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

We would like to apply bias field correction on FLAIR images then
normalize white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the
algorithm has been developed to correct bias field correction in T1 not
clear if it works on FLAIR images.

Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that
includes the processing steps of FLAIR. Is there any link I can use to
upload the file. It gets rejected every time I send it due to size
limitations.

We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.

Thank you
JamesB
___
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 .
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Re: [Freesurfer] White matter normalization

[James Brown]

External Email - Use Caution

Thank you very much for the follow up. I have attached the recon-all.log
once again  for your kind review


Hello James,



I apologize that your message containing the log file got rejected. Can you
please re-send it? I will manually approve it so your conversation with
Doug can continue.



Liam Sennott

On Fri, Sep 16, 2022 at 10:25 AM James Brown  wrote:

> Hi Dr Greeve,
> I greatly apologize if I missed in the log file (attached) how freesurfer
> normalizes flair.  but I couldn't figure it out. Thanks for guidance
>
> James
>
>
>
> can you send your recon-all.log file?
> 
>
>
>
> On Thu, Sep 15, 2022 at 4:04 PM James Brown  wrote:
>
>> Hi Dr Greeve,
>> I ran recon-all using the flag -flair. I couldn't find any command in
>> recon-all.log that normalizes the flair images. It seems just normalization
>> to the T1.
>> I would like to inquire about the flag sigma in the command
>> "mri_normalize" the default is 8. when it is recommended to increase this
>> value? and how much can weincrease it?
>>
>> I'm not sure of the order. You can run recon-all passing in the flair
>> with -flair flair.mgz. At some point in the process it will apply a
>> normalization to the flair (it will not necessarily be the same
>> normalization that is applied to the t1)
>> 
>>
>>
>>
>> On Mon, Sep 12, 2022 at 4:01 PM James Brown  wrote:
>>
>>> Dear Freesurfer experts,
>>> In order to normalize white matter intensity of T1 images and correct
>>> for bias field. I do the following steps:
>>> mri_convert T1.nii.gz T1.mgz
>>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>>
>>> I would like to apply bias field correction on FLAIR images then
>>> normalize white matter intensity.
>>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>>> Reviewing documents about N4biasfieldcorrection I realize that the
>>> algorithm has been developed to correct bias field correction in T1.
>>>
>>> Are the steps above valid for FLAIR images or it can only be applied on
>>> T1 images. We appreciate any feedback about the proper way to correct FLAIR
>>> images for bias field and normalize white matter intensity.
>>>
>>> Thank you
>>> JamesB
>>>
>>>
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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Re: [Freesurfer] White matter normalization

[James Brown]

External Email - Use Caution

I received the email below. any idea how I can send the recon-all log file
to Dr Greeve? Thank you

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On Fri, Sep 16, 2022 at 10:25 AM James Brown  wrote:

> Hi Dr Greeve,
> I greatly apologize if I missed in the log file (attached) how freesurfer
> normalizes flair.  but I couldn't figure it out. Thanks for guidance
>
> James
>
>
>
> can you send your recon-all.log file?
> 
>
>
>
> On Thu, Sep 15, 2022 at 4:04 PM James Brown  wrote:
>
>> Hi Dr Greeve,
>> I ran recon-all using the flag -flair. I couldn't find any command in
>> recon-all.log that normalizes the flair images. It seems just normalization
>> to the T1.
>> I would like to inquire about the flag sigma in the command
>> "mri_normalize" the default is 8. when it is recommended to increase this
>> value? and how much can weincrease it?
>>
>> I'm not sure of the order. You can run recon-all passing in the flair
>> with -flair flair.mgz. At some point in the process it will apply a
>> normalization to the flair (it will not necessarily be the same
>> normalization that is applied to the t1)
>> 
>>
>>
>>
>> On Mon, Sep 12, 2022 at 4:01 PM James Brown  wrote:
>>
>>> Dear Freesurfer experts,
>>> In order to normalize white matter intensity of T1 images and correct
>>> for bias field. I do the following steps:
>>> mri_convert T1.nii.gz T1.mgz
>>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
>>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
>>> mri_convert T1_norm.mgz T1_norm.nii.gz
>>>
>>> I would like to apply bias field correction on FLAIR images then
>>> normalize white matter intensity.
>>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>>> Reviewing documents about N4biasfieldcorrection I realize that the
>>> algorithm has been developed to correct bias field correction in T1.
>>>
>>> Are the steps above valid for FLAIR images or it can only be applied on
>>> T1 images. We appreciate any feedback about the proper way to correct FLAIR
>>> images for bias field and normalize white matter intensity.
>>>
>>> Thank you
>>> JamesB
>>>
>>>
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Re: [Freesurfer] White matter normalization

[James Brown]

External Email - Use Caution

Hi Dr Greeve,
I ran recon-all using the flag -flair. I couldn't find any command in
recon-all.log that normalizes the flair images. It seems just normalization
to the T1.
I would like to inquire about the flag sigma in the command "mri_normalize"
the default is 8. when it is recommended to increase this value? and how
much can weincrease it?

I'm not sure of the order. You can run recon-all passing in the flair with
-flair flair.mgz. At some point in the process it will apply a
normalization to the flair (it will not necessarily be the same
normalization that is applied to the t1)




On Mon, Sep 12, 2022 at 4:01 PM James Brown  wrote:

> Dear Freesurfer experts,
> In order to normalize white matter intensity of T1 images and correct for
> bias field. I do the following steps:
> mri_convert T1.nii.gz T1.mgz
> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
> mri_convert T1_norm.mgz T1_norm.nii.gz
>
> I would like to apply bias field correction on FLAIR images then
> normalize white matter intensity.
> I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
> Reviewing documents about N4biasfieldcorrection I realize that the
> algorithm has been developed to correct bias field correction in T1.
>
> Are the steps above valid for FLAIR images or it can only be applied on T1
> images. We appreciate any feedback about the proper way to correct FLAIR
> images for bias field and normalize white matter intensity.
>
> Thank you
> JamesB
>
>
___
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[Freesurfer] White matter normalization

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for
bias field. I do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz

I would like to apply bias field correction on FLAIR images then
normalize white matter intensity.
I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection I realize that the
algorithm has been developed to correct bias field correction in T1.

Are the steps above valid for FLAIR images or it can only be applied on T1
images. We appreciate any feedback about the proper way to correct FLAIR
images for bias field and normalize white matter intensity.

Thank you
JamesB
___
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 .
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[Freesurfer] Freeview heat map

[James Brown]

External Email - Use Caution

Dear Freesurfer developers,
I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to 
measure a parameter of interest for every ROI in DKT atlas. I would like to 
load the mean values of this parameter to Freeview (every ROI in DKT has one 
value of the parameter represent the mean signal in the ROI). The objective is 
to give color code for every ROI in DKT that fit the values of the computed 
parameter. Is there any way of doing this in Freeview?

Thanks
john___
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Re: [Freesurfer] SNR for PET images

[James Brown]

External Email - Use Caution

Hi Doug, thank you for the response. I would appreciate if you advice any 
better method to compute the SNR for PET signal within an ROI (e..g. thalamus)?
I used spmregister to move my PET images to Freesurfer space then I am thinking 
of using mri_segstat to generate SNR for the PET signal within an ROI, would 
you please suggest an efficient way to do it?

Thank you!

Yes, but know that the "SNR" as computed there is the spatial mean divided by 
the spatial standard dev. This is likely not the SNR that you want

‐‐‐ Original Message ‐‐‐
On August 14, 2018 5:07 PM, James Brown  wrote:

> Hi Freesurfer team,
> I would like to use "mri_segstat" to compute SNR for regions of interest. My 
> question is, if I use PET images as input does this mean that SNR will be 
> computed for the PET signal in the ROIs?
>
> Thanks for any help
> John___
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[Freesurfer] SNR for PET images

[James Brown]

External Email - Use Caution

Hi Freesurfer team,
I would like to use "mri_segstat" to compute SNR for regions of interest. My 
question is, if I use PET images as input does this mean that SNR will be 
computed for the PET signal in the ROIs?

Thanks for any help
John___
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[Freesurfer] Q & A Forum in neuroimaging techniques

[James Brown]

External Email - Use Caution

> Dear Colleagues,
> We would like to create Q & A forum about issues in neuroimaging techniques. 
> Experts from the Martinos Center and Oxford FMRIB will be invited to build 
> this forum and to answer questions and provide plans for critical technical 
> issues. This forum will serve as a reference for our colleagues who would 
> like to learn about neuroimaging  (analyses pipelines, methodologies, tools 
> development. etc) as well as a library and repository that can benefit 
> any one who is interested in this field. The forum will include chat rooms 
> and live discussions with an experts in the field.
>
> We are looking forward for your support and contributions. Please follow us 
> here:
> https://area51.stackexchange.com/proposals/119504/neuroimaging?referrer=JC-CieH5cIdCKHgDAqvZmw2
>
> Sincerely,
> James Brown___
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[Freesurfer] Q & A Forum in neuroimaging techniques

[James Brown]

External Email - Use Caution

Dear Colleagues,
We would like to create Q & A forum about issues in neuroimaging techniques. 
Experts from the Martinos Center and Oxford FMRIB will be invited to build this 
forum and to answer questions and provide plans for critical technical issues. 
This forum will serve as a reference for our colleagues who would like to learn 
about neuroimaging  (analyses pipelines, methodologies, tools development. 
etc) as well as a library and repository that can benefit any one who is 
interested in this field. The forum will include chat rooms and live 
discussions with an experts in the field.

We are looking forward for your support and contributions. Please follow us 
here:
https://area51.stackexchange.com/proposals/119504/neuroimaging?referrer=JC-CieH5cIdCKHgDAqvZmw2

Sincerely,
James Brown___
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