Re: [Freesurfer] Hippocampus Subfields Segmentation

[Douglas N. Greve]

The file with HBT in the name. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


On 5/6/2020 2:14 PM, Muhammad Naveed Iqbal Qureshi wrote:


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Hi FreeSurfer experts,
I preprocess my data with FreeSurfer v 6.
After it I ran developmental version of freesurfer to get the 
hippocampus subfields ROI and volume.

I get the following output:

# Hippocampal subfield volumes as created by segmentHA_T1.sh

1 1  0 618.413010 Hippocampal_tail

2 2  0 308.580548 subiculum-body

3 3  0 112.098146 CA1-body

4 4  0 146.657166 subiculum-head

5 5  0 202.046082 hippocampal-fissure

6 6  0 144.323840 presubiculum-head

7 7  0 513.572092 CA1-head

8 8  0 207.825661 presubiculum-body

9 9  0 75.481830 parasubiculum

10 10  0 332.502880 molecular_layer_HP-head

11 11  0 230.190313 molecular_layer_HP-body

12 12  0 174.264695 GC-ML-DG-head

13 13  0 76.776264 CA3-body

14 14  0 163.024711 GC-ML-DG-body

15 15  0 150.412851 CA4-head

16 16  0 150.002992 CA4-body

17 17  0 85.262570 fimbria

18 18  0 149.769932 CA3-head

19 19  0 61.819269 HATA

20 20  0 1333.761205 Whole_hippocampal_body

21 21  0 1748.804555 Whole_hippocampal_head

22 22  0 3700.978770 Whole_hippocampus



I can see in the hipposubfields.lh.T1.v21.stats and 
lh.hippoSfVolumes-T1.v21.txt files with separate information for the 
head and tail volumes of each subfield.
May I know what is the file name containing the corresponding separate 
head and tail ROIs that were use to calculate the above mentioned volumes?

I can only find full subfield in all the ROI files.

Thank you.
Regards,

Naveed


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[Freesurfer] Hippocampus Subfields Segmentation

[Muhammad Naveed Iqbal Qureshi]

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Hi FreeSurfer experts,
I preprocess my data with FreeSurfer v 6.
After it I ran developmental version of freesurfer to get the hippocampus 
subfields ROI and volume.
I get the following output:


# Hippocampal subfield volumes as created by segmentHA_T1.sh

1 1  0 618.413010 Hippocampal_tail

2 2  0 308.580548 subiculum-body

3 3  0 112.098146 CA1-body

4 4  0 146.657166 subiculum-head

5 5  0 202.046082 hippocampal-fissure

6 6  0 144.323840 presubiculum-head

7 7  0 513.572092 CA1-head

8 8  0 207.825661 presubiculum-body

9 9  0 75.481830 parasubiculum

10 10  0 332.502880 molecular_layer_HP-head

11 11  0 230.190313 molecular_layer_HP-body

12 12  0 174.264695 GC-ML-DG-head

13 13  0 76.776264 CA3-body

14 14  0 163.024711 GC-ML-DG-body

15 15  0 150.412851 CA4-head

16 16  0 150.002992 CA4-body

17 17  0 85.262570 fimbria

18 18  0 149.769932 CA3-head

19 19  0 61.819269 HATA

20 20  0 1333.761205 Whole_hippocampal_body

21 21  0 1748.804555 Whole_hippocampal_head

22 22  0 3700.978770 Whole_hippocampus


I can see in the hipposubfields.lh.T1.v21.stats and 
lh.hippoSfVolumes-T1.v21.txt files with separate information for the head and 
tail volumes of each subfield.
May I know what is the file name containing the corresponding separate head and 
tail ROIs that were use to calculate the above mentioned volumes?
I can only find full subfield in all the ROI files.

Thank you.
Regards,

Naveed
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[Freesurfer] Hippocampus subfields ROI

[Muhammad Naveed Iqbal Qureshi]

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Hi FreeSurfer experts,
I ran developmental version of freesurfer to get the hippocampus subfields ROI 
and volume. I can see in the hipposubfields.lh.T1.v21.stats and 
lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and 
tail volumes of each subfield.
May I know what is the file name containing the corresponding separate 21 head 
and tail ROIs?
I can only find full subfield in all the ROI files.

Thank you.
Regards,

Naveed
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Re: [Freesurfer] Hippocampus subfields outputs missing

[Iglesias Gonzalez, Juan E.]

Dear Naveed,
You need the development version; these files are not given by FreeSurfer 6.0.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Muhammad Naveed 
Iqbal Qureshi 
Reply-To: Freesurfer support list 
Date: Friday, 6 December 2019 at 13:44
To: Freesurfer maillist 
Subject: [Freesurfer] Hippocampus subfields outputs missing


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Hi I ran the following command not the subject on HPC


module load matlab/r2013a

module load freesurfer/6.0.0

source $FREESURFER_HOME/SetUpFreeSurfer.sh

fixup_mni_paths

recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid 
ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd 
/hpf/projects/glongoni/ADHD-200/ -openmp 8


in the output directory I get only following files for both left and right 
hemisphere

lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

lh.hippoSfLabels-T1.v10.mgz

lh.hippoSfVolumes-T1.v10.txt

How can I get following files?

lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz
lh.hippoAmygLabels-T1.v21.CA.mgz
lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz
lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz


I try to find this command but it is not available in my installation


segmentHA_T1.sh

Regards,

Naveed
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[Freesurfer] Hippocampus subfields outputs missing

[Muhammad Naveed Iqbal Qureshi]

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Hi I ran the following command not the subject on HPC


module load matlab/r2013a

module load freesurfer/6.0.0

source $FREESURFER_HOME/SetUpFreeSurfer.sh

fixup_mni_paths

recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid 
ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd 
/hpf/projects/glongoni/ADHD-200/ -openmp 8


in the output directory I get only following files for both left and right 
hemisphere

lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

lh.hippoSfLabels-T1.v10.mgz

lh.hippoSfVolumes-T1.v10.txt

How can I get following files?

lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz
lh.hippoAmygLabels-T1.v21.CA.mgz
lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz
lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz


I try to find this command but it is not available in my installation


segmentHA_T1.sh

Regards,

Naveed
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Re: [Freesurfer] hippocampus subfields with T2

[Iglesias Gonzalez, Eugenio]

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Um this is an empirical question. I would try with and without, and then 
decide.
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Thursday, August 30, 2018 9:38:50 PM
To: Freesurfer support list
Subject: [Freesurfer] hippocampus subfields with T2


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We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic 
T1-mprage and a 1mm isotropic T2-space.
Is it possible or even recommended to try and generate better hippocampal 
segmentation in fressurfer 6.0 using both the T1 and T2,
or does the T2 need to be of equal or better resolution than the T1?

Jim


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[Freesurfer] hippocampus subfields with T2

[Alexopoulos, Dimitrios]

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We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic 
T1-mprage and a 1mm isotropic T2-space.
Is it possible or even recommended to try and generate better hippocampal 
segmentation in fressurfer 6.0 using both the T1 and T2,
or does the T2 need to be of equal or better resolution than the T1?

Jim


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] hippocampus subfields and manual editing

[Iglesias Gonzalez, Eugenio]

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Hi Lara,
A little trick you can do (it shouldn’t be too hard to implement in Matlab with 
the functions in $FREESURFER_HOME/matlab)
For each subject:
1. make a copy of aseg.mgz
2. create a binary mask for your edited hippocampi.
3. in aseg.mgz, replace each voxel labeled as hippo by the label of the 
closest, non-hippocampal structure.
4. Paint your hippocampi from step 2 on the hippocampal-less aseg.
I hope this helps,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 13/06/2018, 17:18, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lara 
Foland-Ross"  wrote:

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Hello, 

I am running an analysis of hippocampus volume on a set of T1-weighted 
scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a 
moderate degree of manual editing was required to correct the boundaries of 
each subject's hippocampus. 

Final volumes of manually edited hippocampi were submitted to a repeated 
measures ANOVA which showed a significant main effect of diagnosis on the 
overall size of this structure (controlling for age and TBV).

We recently submitted this paper and just received a request from a 
reviewer that asked that we run a subfield analysis on these data to better 
understand the regions driving this overall effect. 

What I'd like to know is: would the subfield approach *not* be recommended 
on this dataset considering that artifacts necessitated a good deal of manual 
intervention for the entire region? Second, if it a subfield approach *is* okay 
to run on these data, how can I feed in my manually edited volumes to ensure 
that the corrected segmentations of the entire hippocampus is used during 
subfield creation?

thanks very much in advance!
Lara


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



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[Freesurfer] hippocampus subfields and manual editing

[Lara Foland-Ross]

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Hello, 

I am running an analysis of hippocampus volume on a set of T1-weighted scans 
with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate 
degree of manual editing was required to correct the boundaries of each 
subject's hippocampus. 

Final volumes of manually edited hippocampi were submitted to a repeated 
measures ANOVA which showed a significant main effect of diagnosis on the 
overall size of this structure (controlling for age and TBV).

We recently submitted this paper and just received a request from a reviewer 
that asked that we run a subfield analysis on these data to better understand 
the regions driving this overall effect. 

What I'd like to know is: would the subfield approach *not* be recommended on 
this dataset considering that artifacts necessitated a good deal of manual 
intervention for the entire region? Second, if it a subfield approach *is* okay 
to run on these data, how can I feed in my manually edited volumes to ensure 
that the corrected segmentations of the entire hippocampus is used during 
subfield creation?

thanks very much in advance!
Lara


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



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[Freesurfer] Hippocampus subfields {Disarmed}

[郑凤莲]

Hi Experts,

I ran the segmentation of hippocampus in Freesurfer dev version. The left or 
right whole volume isn't equal to the sum of 12 subfields. But it is equal to 
the sum of the volume of tail, whole head and body. Why?
 I am looking forward to your reply. Thank you very much.

Sincerely,
Zheng



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13181786167
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Re: [Freesurfer] hippocampus subfields

[Iglesias Gonzalez, Eugenio]

Dear Zheng,
You can build a GLM with a  single group, and then look at the residuals. Or, 
even easier: just divide the volumes of each subject by his/her ICV (the 
answers won’t be identical, but should definitely be quite similar).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 1 December 2017 at 12:55
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer]  hippocampus subfields

Hi Bruce,

I am sorry for asking you question as this, but I really don't know how to 
do it?
It seems that GLM is suitable for there are two groups or more. But I only 
have one group, If I want to get the line trend with eTIV corrected for the 
relationship between age and volume, what should I do?
The  picture is my result, but it doesn't corrected by eTIV. I appreciate your 
help, please.
[cid:image001.png@01D36AA7.7A149BD0]

Thanks a lot!
Zheng





At 2017-11-22 10:29:43, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:

>you would include it as a nuisance variable in the glm

>On Wed, 22 Nov 2017,

>郑凤莲 wrote:

>

>> Hi Bruce,

>>

>>  Thanks for your quick reply. These results are not correted by eTIV, If 
>> eTIV are corrected, I

>> can only get the p value and scatter plot, I can't get the line trend. Do 
>> you know how to get the

>> line trend with eTIV corrected as these results?

>>

>> Thanks,

>> Zheng

>>

>>

>>

>>

>>

>> 在 2017-11-22 10:14:16，"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> 写道：

>> >is this eTIV corrected? I would look at some of the outliers and make

>> >sure that the segmentations are accurate. Certainly the trend is in the

>> >correct (and depressing) direction.

>> >

>> >cheers

>> >Bruce

>> >On Wed, 22 Nov 2017, 郑凤莲 wrote:

>> >

>> >> Hi Bruce,

>> >>

>> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> stands women, and Red colo

>> r

>> >> stands men.

>> >> The number of the data is not enough large. Are they ok? May I use 
>> >> them in my paper?

>> >> [IMAGE][IMAGE][IMAGE]

>> >>

>> >>

>> >> Thanks a lot !

>> >> Zheng

>> >>

>> >>

>> >>

>> >>

>> >> At 2017-11-20 10:15:49, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:

>> >> >Hi Zheng

>> >> >

>> >> >I would scatter plot age vs. volume, coloring men and women differently

>> >> >(or different symbols) with and without eTIV correction to get an idea of

>> >> >what is going on

>> >> >

>> >> >cheers

>> >> >Bruce

>> >> >

>> >> >

>> >> >On Mon, 20 Nov

>> >> >2017, 郑凤莲 wrote:

>> >> >

>> >> >> Hi Bruce,

>> >> >>

>> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  well 
>> >> >> from 40 to 55 and from 56

>>  to

>> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> know how I can explain this

>> >> >> problem.

>> >> >>   Thanks again.

>> >> >>

>> >> >> Sincerely,

>> >> >> Zheng

>> >> >>

>> >> >>

>> >> >>

>> >> >>

>> >> >>

>> >> >> At 2017-11-20 09:35:45, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> 
>> >> >> wrote:

>> >> >> >Hi Zheng

>> >> >> >

>> >> >> >how uniform is your distribution? I'm hardly an expert on this, but I

>> >> >> >wouldn't expect very large effects until you get into the older end of

>> >> >> >that range. Have you scatter plotted your data?

>> >> >> >Bruce

>> >> >> >On Mon, 20 Nov 2017, 郑凤莲

>> >> >> >wrote:

>> >> >> >

>> >> >> >>

>> >> >> >> Hi Bruce,

>> >> >> >>

>> >> >> >>

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


I am sorry for asking you question as this, but I really don't know how to 
do it?
It seems that GLM is suitable for there are two groups or more. But I only 
have one group, If I want to get the line trend with eTIV corrected for the 
relationship between age and volume, what should I do?
The  picture is my result, but it doesn't corrected by eTIV. I appreciate your 
help, please.


Thanks a lot!
Zheng








At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>you would include it as a nuisance variable in the glm
>On Wed, 22 Nov 2017, 
>郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>>  Thanks for your quick reply. These results are not correted by eTIV, If 
>> eTIV are corrected, I
>> can only get the p value and scatter plot, I can't get the line trend. Do 
>> you know how to get the
>> line trend with eTIV corrected as these results?
>> 
>> Thanks,
>> Zheng 
>> 
>> 
>> 
>> 
>> 
>> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >is this eTIV corrected? I would look at some of the outliers and make 
>> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >correct (and depressing) direction.
>> >
>> >cheers
>> >Bruce
>> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> stands women, and Red colo
>> r
>> >> stands men.
>> >> The number of the data is not enough large. Are they ok? May I use 
>> >> them in my paper?
>> >> [IMAGE][IMAGE][IMAGE]
>> >> 
>> >> 
>> >> Thanks a lot !
>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:
>> >> >Hi Zheng
>> >> >
>> >> >I would scatter plot age vs. volume, coloring men and women differently 
>> >> >(or different symbols) with and without eTIV correction to get an idea 
>> >> >of 
>> >> >what is going on
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >
>> >> >
>> >> >On Mon, 20 Nov 
>> >> >2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >>  
>> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  well 
>> >> >> from 40 to 55 and from 56
>>  to
>> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> know how I can explain this
>> >> >> problem. 
>> >> >>   Thanks again.
>> >> >> 
>> >> >> Sincerely,
>> >> >> Zheng  
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >> >> >wouldn't expect very large effects until you get into the older end 
>> >> >> >of 
>> >> >> >that range. Have you scatter plotted your data?
>> >> >> >Bruce
>> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >wrote:
>> >> >> >
>> >> >> >> 
>> >> >> >> Hi Bruce,
>> >> >> >> 
>> >> >> >> Thank you for your help.
>> >> >> >> I have  54 subjects, aged from 21 to 71 and only one group. I 
>> >> >> >> want to compare the chang
>> e o
>> >> f
>> >> >> >> hippocampus volume with age. The results before and after doing the 
>> >> >> >> correction for eTIV are
>>  th
>> >> e
>> >> >> >> same. Where is wrong? Or if there is no error, how can I explain it 
>> >> >> >> in discussion?
>> >> >> >> 
>> >> >> >> Thanks,
>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power to 
>> >> >> >> >see, or 
>> >> >> >> >there is no effect? You would need to give us more details for us 
>> >> >> >> >to help. 
>> >> >> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >> >> >
>> >> >> >> >cheers
>> >> >> >> >Bruce
>> >> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >>  I am sorry for this situation. 
>> >> >> >> >>  In the first way, there was an statistical difference in 
>> >> >> >> >> left hippocampus, but no d
>> iff
>> >> ere
>> >> >> nce
>> >> >> >>  in
>> >> >> >> >> right hippocampus. In the second way, there was both no 
>> >> >> >> >> statistical difference in left o
>> r
>> >> >> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >> >> >>  Can you understand me this time?
>> >> >> >> >> 
>> >> >> >> >> Thanks,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-18 22:58:56, "Bruce Fischl" 
>> >> >> >> >>  wrote:
>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >no difference between what and what?
>> >> >> >> >> >
>> >> >> >> >> >cheers
>> >> >> >> >> >Bruce
>> >> >> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >> >
>> >> >> >> >> >> Hi professor,
>> >> >> >> >> >> 
>> >> >> 

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,
It's OK. Thank you very much for your reply ! I will find it in other way.


Sincerely,
Zheng






At 2017-11-23 11:37:37, "Bruce Fischl"  wrote:

Sorry, I don’t remember. You can search on the wiki or maybe someone else will 
chime in
Bruce

On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...@163.com> wrote:


Hi Bruce,

Could tell me which is the whole brain volume,please? I'm not sure which is 
right. I need your help.


Thanks very much.
Zheng








At 2017-11-22 11:07:36, "Bruce Fischl"  wrote:
>no, eTIV is the estimated volume of the intracranial vault, so it 
>included sulcal CSF. I think we include a whole brain volume in the 
>aseg.stats file that you can use, although I don't remember what it's 
>called
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> Thank you very much. I will try it. And I have another question. I also 
>> want to study the
>> relation between age and the whole brain volume, gray matter volume and 
>> white matter volume. The
>> whole brain volume is the same as eTIV, is right?
>> 
>> Thanks,
>> Zheng
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>> >you would include it as a nuisance variable in the glm
>> >On Wed, 22 Nov 2017, 
>> >郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>  Thanks for your quick reply. These results are not correted by eTIV, 
>> >> If eTIV are corrected, 
>> I
>> >> can only get the p value and scatter plot, I can't get the line trend. Do 
>> >> you know how to get the
>> >> line trend with eTIV corrected as these results?
>> >> 
>> >> Thanks,
>> >> Zheng 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >> >is this eTIV corrected? I would look at some of the outliers and make 
>> >> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >> >correct (and depressing) direction.
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >> 
>> >> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> >> stands women, and Red c
>> olo
>> >> r
>> >> >> stands men.
>> >> >> The number of the data is not enough large. Are they ok? May I use 
>> >> >> them in my paper?
>> >> >> [IMAGE][IMAGE][IMAGE]
>> >> >> 
>> >> >> 
>> >> >> Thanks a lot !
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 10:15:49, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >I would scatter plot age vs. volume, coloring men and women 
>> >> >> >differently 
>> >> >> >(or different symbols) with and without eTIV correction to get an 
>> >> >> >idea of 
>> >> >> >what is going on
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >
>> >> >> >
>> >> >> >On Mon, 20 Nov 
>> >> >> >2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi Bruce,
>> >> >> >>  
>> >> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  
>> >> >> >> well from 40 to 55 and from
>>  56
>> >>  to
>> >> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> >> know how I can explain t
>> his
>> >> >> >> problem. 
>> >> >> >>   Thanks again.
>> >> >> >> 
>> >> >> >> Sincerely,
>> >> >> >> Zheng  
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >how uniform is your distribution? I'm hardly an expert on this, 
>> >> >> >> >but I 
>> >> >> >> >wouldn't expect very large effects until you get into the older 
>> >> >> >> >end of 
>> >> >> >> >that range. Have you scatter plotted your data?
>> >> >> >> >Bruce
>> >> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >> >wrote:
>> >> >> >> >
>> >> >> >> >> 
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >> Thank you for your help.
>> >> >> >> >> I have  54 subjects, aged from 21 to 71 and only one group. 
>> >> >> >> >> I want to compare the ch
>> ang
>> >> e o
>> >> >> f
>> >> >> >> >> hippocampus volume with age. The results before and after doing 
>> >> >> >> >> the correction for eTIV 
>> are
>> >>  th
>> >> >> e
>> >> >> >> >> same. Where is wrong? Or if there is no error, how can I explain 
>> >> >> >> >> it in discussion?
>> >> >> >> >> 
>> >> >> >> >> Thanks,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl" 
>> >> >> >> >>  wrote:
>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power 
>> >> >> >> >> >to see, or 
>> >> >> >> >> >there is no effect? You would need to give us more details for 
>> >> >> >> >> >us to help. 
>> >> >> >> >> >Are you correcting for eTIV? What measure are you 

Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

Sorry, I don’t remember. You can search on the wiki or maybe someone else will 
chime in
Bruce

> On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...@163.com> wrote:
> 
> Hi Bruce,
> 
> Could tell me which is the whole brain volume,please? I'm not sure which 
> is right. I need your help.
> 
> Thanks very much.
> Zheng
> 
> 
> 
> 
> 
> 
> At 2017-11-22 11:07:36, "Bruce Fischl"  wrote:
> >no, eTIV is the estimated volume of the intracranial vault, so it 
> >included sulcal CSF. I think we include a whole brain volume in the 
> >aseg.stats file that you can use, although I don't remember what it's 
> >called
> >
> >cheers
> >Bruce
> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
> >
> >> Hi Bruce,
> >> Thank you very much. I will try it. And I have another question. I 
> >> also want to study the
> >> relation between age and the whole brain volume, gray matter volume and 
> >> white matter volume. The
> >> whole brain volume is the same as eTIV, is right?
> >> 
> >> Thanks,
> >> Zheng
> >> 
> >> 
> >> 
> >> 
> >> 
> >> At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
> >> >you would include it as a nuisance variable in the glm
> >> >On Wed, 22 Nov 2017, 
> >> >郑凤莲 wrote:
> >> >
> >> >> Hi Bruce,
> >> >> 
> >> >>  Thanks for your quick reply. These results are not correted by 
> >> >> eTIV, If eTIV are corrected, 
> >> I
> >> >> can only get the p value and scatter plot, I can't get the line trend. 
> >> >> Do you know how to get the
> >> >> line trend with eTIV corrected as these results?
> >> >> 
> >> >> Thanks,
> >> >> Zheng 
> >> >> 
> >> >> 
> >> >> 
> >> >> 
> >> >> 
> >> >> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
> >> >> >is this eTIV corrected? I would look at some of the outliers and make 
> >> >> >sure that the segmentations are accurate. Certainly the trend is in 
> >> >> >the 
> >> >> >correct (and depressing) direction.
> >> >> >
> >> >> >cheers
> >> >> >Bruce
> >> >> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
> >> >> >
> >> >> >> Hi Bruce,
> >> >> >> 
> >> >> >> Thanks for your advice. There are a part of the result. Blue 
> >> >> >> color stands women, and Red c
> >> olo
> >> >> r
> >> >> >> stands men.
> >> >> >> The number of the data is not enough large. Are they ok? May I 
> >> >> >> use them in my paper?
> >> >> >> [IMAGE][IMAGE][IMAGE]
> >> >> >> 
> >> >> >> 
> >> >> >> Thanks a lot !
> >> >> >> Zheng
> >> >> >> 
> >> >> >> 
> >> >> >> 
> >> >> >> 
> >> >> >> At 2017-11-20 10:15:49, "Bruce Fischl"  
> >> >> >> wrote:
> >> >> >> >Hi Zheng
> >> >> >> >
> >> >> >> >I would scatter plot age vs. volume, coloring men and women 
> >> >> >> >differently 
> >> >> >> >(or different symbols) with and without eTIV correction to get an 
> >> >> >> >idea of 
> >> >> >> >what is going on
> >> >> >> >
> >> >> >> >cheers
> >> >> >> >Bruce
> >> >> >> >
> >> >> >> >
> >> >> >> >On Mon, 20 Nov 
> >> >> >> >2017, 郑凤莲 wrote:
> >> >> >> >
> >> >> >> >> Hi Bruce,
> >> >> >> >>  
> >> >> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  
> >> >> >> >> well from 40 to 55 and from
> >>  56
> >> >>  to
> >> >> >> >> 71. I did the correlation analysis between age and volume. I 
> >> >> >> >> don't know how I can explain t
> >> his
> >> >> >> >> problem. 
> >> >> >> >>   Thanks again.
> >> >> >> >> 
> >> >> >> >> Sincerely,
> >> >> >> >> Zheng  
> >> >> >> >> 
> >> >> >> >> 
> >> >> >> >> 
> >> >> >> >> 
> >> >> >> >> 
> >> >> >> >> At 2017-11-20 09:35:45, "Bruce Fischl" 
> >> >> >> >>  wrote:
> >> >> >> >> >Hi Zheng
> >> >> >> >> >
> >> >> >> >> >how uniform is your distribution? I'm hardly an expert on this, 
> >> >> >> >> >but I 
> >> >> >> >> >wouldn't expect very large effects until you get into the older 
> >> >> >> >> >end of 
> >> >> >> >> >that range. Have you scatter plotted your data?
> >> >> >> >> >Bruce
> >> >> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
> >> >> >> >> >wrote:
> >> >> >> >> >
> >> >> >> >> >> 
> >> >> >> >> >> Hi Bruce,
> >> >> >> >> >> 
> >> >> >> >> >> Thank you for your help.
> >> >> >> >> >> I have  54 subjects, aged from 21 to 71 and only one 
> >> >> >> >> >> group. I want to compare the ch
> >> ang
> >> >> e o
> >> >> >> f
> >> >> >> >> >> hippocampus volume with age. The results before and after 
> >> >> >> >> >> doing the correction for eTIV 
> >> are
> >> >>  th
> >> >> >> e
> >> >> >> >> >> same. Where is wrong? Or if there is no error, how can I 
> >> >> >> >> >> explain it in discussion?
> >> >> >> >> >> 
> >> >> >> >> >> Thanks,
> >> >> >> >> >> Zheng
> >> >> >> >> >> 
> >> >> >> >> >> 
> >> >> >> >> >> 
> >> >> >> >> >> 
> >> >> >> >> >> 
> >> >> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl" 
> >> >> >> >> >>  wrote:
> >> >> >> >> >> >Hi Zheng
> >> >> >> >> >> >
> >> >> >> >> >> >yes, I see. Maybe the effect is smaller than you have the 
> >> >> >> >> >> >power to see, or 
> >> >> >> >> >> 

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,

Could tell me which is the whole brain volume,please? I'm not sure which is 
right. I need your help.


Thanks very much.
Zheng








At 2017-11-22 11:07:36, "Bruce Fischl"  wrote:
>no, eTIV is the estimated volume of the intracranial vault, so it 
>included sulcal CSF. I think we include a whole brain volume in the 
>aseg.stats file that you can use, although I don't remember what it's 
>called
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> Thank you very much. I will try it. And I have another question. I also 
>> want to study the
>> relation between age and the whole brain volume, gray matter volume and 
>> white matter volume. The
>> whole brain volume is the same as eTIV, is right?
>> 
>> Thanks,
>> Zheng
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>> >you would include it as a nuisance variable in the glm
>> >On Wed, 22 Nov 2017, 
>> >郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>  Thanks for your quick reply. These results are not correted by eTIV, 
>> >> If eTIV are corrected, 
>> I
>> >> can only get the p value and scatter plot, I can't get the line trend. Do 
>> >> you know how to get the
>> >> line trend with eTIV corrected as these results?
>> >> 
>> >> Thanks,
>> >> Zheng 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >> >is this eTIV corrected? I would look at some of the outliers and make 
>> >> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >> >correct (and depressing) direction.
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >> 
>> >> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> >> stands women, and Red c
>> olo
>> >> r
>> >> >> stands men.
>> >> >> The number of the data is not enough large. Are they ok? May I use 
>> >> >> them in my paper?
>> >> >> [IMAGE][IMAGE][IMAGE]
>> >> >> 
>> >> >> 
>> >> >> Thanks a lot !
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 10:15:49, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >I would scatter plot age vs. volume, coloring men and women 
>> >> >> >differently 
>> >> >> >(or different symbols) with and without eTIV correction to get an 
>> >> >> >idea of 
>> >> >> >what is going on
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >
>> >> >> >
>> >> >> >On Mon, 20 Nov 
>> >> >> >2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi Bruce,
>> >> >> >>  
>> >> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  
>> >> >> >> well from 40 to 55 and from
>>  56
>> >>  to
>> >> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> >> know how I can explain t
>> his
>> >> >> >> problem. 
>> >> >> >>   Thanks again.
>> >> >> >> 
>> >> >> >> Sincerely,
>> >> >> >> Zheng  
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >how uniform is your distribution? I'm hardly an expert on this, 
>> >> >> >> >but I 
>> >> >> >> >wouldn't expect very large effects until you get into the older 
>> >> >> >> >end of 
>> >> >> >> >that range. Have you scatter plotted your data?
>> >> >> >> >Bruce
>> >> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >> >wrote:
>> >> >> >> >
>> >> >> >> >> 
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >> Thank you for your help.
>> >> >> >> >> I have  54 subjects, aged from 21 to 71 and only one group. 
>> >> >> >> >> I want to compare the ch
>> ang
>> >> e o
>> >> >> f
>> >> >> >> >> hippocampus volume with age. The results before and after doing 
>> >> >> >> >> the correction for eTIV 
>> are
>> >>  th
>> >> >> e
>> >> >> >> >> same. Where is wrong? Or if there is no error, how can I explain 
>> >> >> >> >> it in discussion?
>> >> >> >> >> 
>> >> >> >> >> Thanks,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl" 
>> >> >> >> >>  wrote:
>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power 
>> >> >> >> >> >to see, or 
>> >> >> >> >> >there is no effect? You would need to give us more details for 
>> >> >> >> >> >us to help. 
>> >> >> >> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >> >> >> >
>> >> >> >> >> >cheers
>> >> >> >> >> >Bruce
>> >> >> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >> >
>> >> >> >> >> >> Hi Bruce,
>> >> >> >> >> >> 
>> >> >> >> >> >>  I am sorry for this situation. 
>> >> >> >> >> >>  In the first way, there was an statistical difference in 
>> >> >> >> >> >> left 

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


 There is aseg.stats. Is it brain segmentation volume? 

 And in QDEC, I study the relationship between age and the cortical 
thickness, volume and surface area. The eTIV for  volume and surface area 
should be set in Nuisance Factors, but for thickness, it's not need. Is right?


Thanks,
Zheng







At 2017-11-22 11:07:36, "Bruce Fischl"  wrote:
>no, eTIV is the estimated volume of the intracranial vault, so it 
>included sulcal CSF. I think we include a whole brain volume in the 
>aseg.stats file that you can use, although I don't remember what it's 
>called
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> Thank you very much. I will try it. And I have another question. I also 
>> want to study the
>> relation between age and the whole brain volume, gray matter volume and 
>> white matter volume. The
>> whole brain volume is the same as eTIV, is right?
>> 
>> Thanks,
>> Zheng
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>> >you would include it as a nuisance variable in the glm
>> >On Wed, 22 Nov 2017, 
>> >郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>  Thanks for your quick reply. These results are not correted by eTIV, 
>> >> If eTIV are corrected, 
>> I
>> >> can only get the p value and scatter plot, I can't get the line trend. Do 
>> >> you know how to get the
>> >> line trend with eTIV corrected as these results?
>> >> 
>> >> Thanks,
>> >> Zheng 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >> >is this eTIV corrected? I would look at some of the outliers and make 
>> >> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >> >correct (and depressing) direction.
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >> 
>> >> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> >> stands women, and Red c
>> olo
>> >> r
>> >> >> stands men.
>> >> >> The number of the data is not enough large. Are they ok? May I use 
>> >> >> them in my paper?
>> >> >> [IMAGE][IMAGE][IMAGE]
>> >> >> 
>> >> >> 
>> >> >> Thanks a lot !
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 10:15:49, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >I would scatter plot age vs. volume, coloring men and women 
>> >> >> >differently 
>> >> >> >(or different symbols) with and without eTIV correction to get an 
>> >> >> >idea of 
>> >> >> >what is going on
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >
>> >> >> >
>> >> >> >On Mon, 20 Nov 
>> >> >> >2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi Bruce,
>> >> >> >>  
>> >> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  
>> >> >> >> well from 40 to 55 and from
>>  56
>> >>  to
>> >> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> >> know how I can explain t
>> his
>> >> >> >> problem. 
>> >> >> >>   Thanks again.
>> >> >> >> 
>> >> >> >> Sincerely,
>> >> >> >> Zheng  
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >how uniform is your distribution? I'm hardly an expert on this, 
>> >> >> >> >but I 
>> >> >> >> >wouldn't expect very large effects until you get into the older 
>> >> >> >> >end of 
>> >> >> >> >that range. Have you scatter plotted your data?
>> >> >> >> >Bruce
>> >> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >> >wrote:
>> >> >> >> >
>> >> >> >> >> 
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >> Thank you for your help.
>> >> >> >> >> I have  54 subjects, aged from 21 to 71 and only one group. 
>> >> >> >> >> I want to compare the ch
>> ang
>> >> e o
>> >> >> f
>> >> >> >> >> hippocampus volume with age. The results before and after doing 
>> >> >> >> >> the correction for eTIV 
>> are
>> >>  th
>> >> >> e
>> >> >> >> >> same. Where is wrong? Or if there is no error, how can I explain 
>> >> >> >> >> it in discussion?
>> >> >> >> >> 
>> >> >> >> >> Thanks,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl" 
>> >> >> >> >>  wrote:
>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power 
>> >> >> >> >> >to see, or 
>> >> >> >> >> >there is no effect? You would need to give us more details for 
>> >> >> >> >> >us to help. 
>> >> >> >> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >> >> >> >
>> >> >> >> >> >cheers
>> >> >> >> >> >Bruce
>> >> >> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >> >
>> >> >> >> >> >> Hi Bruce,
>> >> >> 

Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

no, eTIV is the estimated volume of the intracranial vault, so it 
included sulcal CSF. I think we include a whole brain volume in the 
aseg.stats file that you can use, although I don't remember what it's 
called


cheers
Bruce
On Wed, 22 Nov 2017, 郑凤莲 wrote:


Hi Bruce,
    Thank you very much. I will try it. And I have another question. I also 
want to study the
relation between age and the whole brain volume, gray matter volume and white 
matter volume. The
whole brain volume is the same as eTIV, is right?

Thanks,
Zheng





At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>you would include it as a nuisance variable in the glm
>On Wed, 22 Nov 2017, 
>郑凤莲 wrote:

>
>> Hi Bruce,
>> 
>>      Thanks for your quick reply. These results are not correted by eTIV, If eTIV are corrected, 
I

>> can only get the p value and scatter plot, I can't get the line trend. Do 
you know how to get the
>> line trend with eTIV corrected as these results?
>> 
>> Thanks,

>> Zheng 
>> 
>> 
>> 
>> 
>> 
>> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >is this eTIV corrected? I would look at some of the outliers and make 
>> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >correct (and depressing) direction.

>> >
>> >cheers
>> >Bruce
>> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>     Thanks for your advice. There are a part of the result. Blue color stands women, and Red c

olo
>> r
>> >> stands men.
>> >>     The number of the data is not enough large. Are they ok? May I use 
them in my paper?
>> >> [IMAGE][IMAGE][IMAGE]
>> >> 
>> >> 
>> >> Thanks a lot !

>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:

>> >> >Hi Zheng
>> >> >
>> >> >I would scatter plot age vs. volume, coloring men and women differently 
>> >> >(or different symbols) with and without eTIV correction to get an idea of 
>> >> >what is going on

>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >
>> >> >
>> >> >On Mon, 20 Nov 
>> >> >2017, 郑凤莲 wrote:

>> >> >
>> >> >> Hi Bruce,
>> >> >>  
>> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  well 
from 40 to 55 and from
 56
>>  to
>> >> >> 71. I did the correlation analysis between age and volume. I don't 
know how I can explain t
his
>> >> >> problem. 
>> >> >>   Thanks again.
>> >> >> 
>> >> >> Sincerely,

>> >> >> Zheng  
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:

>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >> >> >wouldn't expect very large effects until you get into the older end of 
>> >> >> >that range. Have you scatter plotted your data?

>> >> >> >Bruce
>> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >wrote:

>> >> >> >
>> >> >> >> 
>> >> >> >> Hi Bruce,
>> >> >> >> 
>> >> >> >>     Thank you for your help.

>> >> >> >>     I have  54 subjects, aged from 21 to 71 and only one group. I 
want to compare the ch
ang
>> e o
>> >> f
>> >> >> >> hippocampus volume with age. The results before and after doing the correction for eTIV 
are

>>  th
>> >> e
>> >> >> >> same. Where is wrong? Or if there is no error, how can I explain it 
in discussion?
>> >> >> >> 
>> >> >> >> Thanks,

>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:

>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power to see, or 
>> >> >> >> >there is no effect? You would need to give us more details for us to help. 
>> >> >> >> >Are you correcting for eTIV? What measure are you comparing?

>> >> >> >> >
>> >> >> >> >cheers
>> >> >> >> >Bruce
>> >> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >>      I am sorry for this situation. 

>> >> >> >> >>      In the first way, there was an statistical difference in 
left hippocampus, but n
o d
>> iff
>> >> ere
>> >> >> nce
>> >> >> >>  in
>> >> >> >> >> right hippocampus. In the second way, there was both no 
statistical difference in lef
t o
>> r
>> >> >> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >> >> >>      Can you understand me this time?
>> >> >> >> >> 
>> >> >> >> >> Thanks,

>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:

>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >no difference between what and what?
>> >> >> >> >> >
>> >> >> >> >> >cheers
>> >> >> >> >> >Bruce
>> >> >> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >> >
>> >> >> >> >> >> Hi professor,
>> >> >> >> >> >> 
>> >> >> >> >> >>     I am using Freesurfer for DTI data. When I run 

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,
Thank you very much. I will try it. And I have another question. I also 
want to study the relation between age and the whole brain volume, gray matter 
volume and white matter volume. The whole brain volume is the same as eTIV, is 
right?


Thanks,
Zheng








At 2017-11-22 10:29:43, "Bruce Fischl"  wrote:
>you would include it as a nuisance variable in the glm
>On Wed, 22 Nov 2017, 
>郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>>  Thanks for your quick reply. These results are not correted by eTIV, If 
>> eTIV are corrected, I
>> can only get the p value and scatter plot, I can't get the line trend. Do 
>> you know how to get the
>> line trend with eTIV corrected as these results?
>> 
>> Thanks,
>> Zheng 
>> 
>> 
>> 
>> 
>> 
>> 在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>> >is this eTIV corrected? I would look at some of the outliers and make 
>> >sure that the segmentations are accurate. Certainly the trend is in the 
>> >correct (and depressing) direction.
>> >
>> >cheers
>> >Bruce
>> >On Wed, 22 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >> Thanks for your advice. There are a part of the result. Blue color 
>> >> stands women, and Red colo
>> r
>> >> stands men.
>> >> The number of the data is not enough large. Are they ok? May I use 
>> >> them in my paper?
>> >> [IMAGE][IMAGE][IMAGE]
>> >> 
>> >> 
>> >> Thanks a lot !
>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:
>> >> >Hi Zheng
>> >> >
>> >> >I would scatter plot age vs. volume, coloring men and women differently 
>> >> >(or different symbols) with and without eTIV correction to get an idea 
>> >> >of 
>> >> >what is going on
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >
>> >> >
>> >> >On Mon, 20 Nov 
>> >> >2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >>  
>> >> >>   My data is loss from 35 to 40. But the uniform of sex is not  well 
>> >> >> from 40 to 55 and from 56
>>  to
>> >> >> 71. I did the correlation analysis between age and volume. I don't 
>> >> >> know how I can explain this
>> >> >> problem. 
>> >> >>   Thanks again.
>> >> >> 
>> >> >> Sincerely,
>> >> >> Zheng  
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 09:35:45, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >> >> >wouldn't expect very large effects until you get into the older end 
>> >> >> >of 
>> >> >> >that range. Have you scatter plotted your data?
>> >> >> >Bruce
>> >> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >> >wrote:
>> >> >> >
>> >> >> >> 
>> >> >> >> Hi Bruce,
>> >> >> >> 
>> >> >> >> Thank you for your help.
>> >> >> >> I have  54 subjects, aged from 21 to 71 and only one group. I 
>> >> >> >> want to compare the chang
>> e o
>> >> f
>> >> >> >> hippocampus volume with age. The results before and after doing the 
>> >> >> >> correction for eTIV are
>>  th
>> >> e
>> >> >> >> same. Where is wrong? Or if there is no error, how can I explain it 
>> >> >> >> in discussion?
>> >> >> >> 
>> >> >> >> Thanks,
>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-20 04:55:49, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >yes, I see. Maybe the effect is smaller than you have the power to 
>> >> >> >> >see, or 
>> >> >> >> >there is no effect? You would need to give us more details for us 
>> >> >> >> >to help. 
>> >> >> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >> >> >
>> >> >> >> >cheers
>> >> >> >> >Bruce
>> >> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >
>> >> >> >> >> Hi Bruce,
>> >> >> >> >> 
>> >> >> >> >>  I am sorry for this situation. 
>> >> >> >> >>  In the first way, there was an statistical difference in 
>> >> >> >> >> left hippocampus, but no d
>> iff
>> >> ere
>> >> >> nce
>> >> >> >>  in
>> >> >> >> >> right hippocampus. In the second way, there was both no 
>> >> >> >> >> statistical difference in left o
>> r
>> >> >> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >> >> >>  Can you understand me this time?
>> >> >> >> >> 
>> >> >> >> >> Thanks,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> At 2017-11-18 22:58:56, "Bruce Fischl" 
>> >> >> >> >>  wrote:
>> >> >> >> >> >Hi Zheng
>> >> >> >> >> >
>> >> >> >> >> >no difference between what and what?
>> >> >> >> >> >
>> >> >> >> >> >cheers
>> >> >> >> >> >Bruce
>> >> >> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >> >
>> >> >> >> >> >> Hi professor,
>> >> >> >> >> >> 
>> >> >> >> >> >> I am using Freesurfer for DTI data. When I run 
>> >> >> >> >> >> 'mri_segstats', I 
>> >> >> >> >> >> got the result that there w
>> >> >> >> 

Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

you would include it as a nuisance variable in the glm
On Wed, 22 Nov 2017, 
郑凤莲 wrote:



Hi Bruce,

     Thanks for your quick reply. These results are not correted by eTIV, If 
eTIV are corrected, I
can only get the p value and scatter plot, I can't get the line trend. Do you 
know how to get the
line trend with eTIV corrected as these results?

Thanks,
Zheng 





在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>is this eTIV corrected? I would look at some of the outliers and make 
>sure that the segmentations are accurate. Certainly the trend is in the 
>correct (and depressing) direction.

>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>>     Thanks for your advice. There are a part of the result. Blue color stands women, and Red colo

r
>> stands men.
>>     The number of the data is not enough large. Are they ok? May I use them 
in my paper?
>> [IMAGE][IMAGE][IMAGE]
>> 
>> 
>> Thanks a lot !

>> Zheng
>> 
>> 
>> 
>> 
>> At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:

>> >Hi Zheng
>> >
>> >I would scatter plot age vs. volume, coloring men and women differently 
>> >(or different symbols) with and without eTIV correction to get an idea of 
>> >what is going on

>> >
>> >cheers
>> >Bruce
>> >
>> >
>> >On Mon, 20 Nov 
>> >2017, 郑凤莲 wrote:

>> >
>> >> Hi Bruce,
>> >>  
>> >>   My data is loss from 35 to 40. But the uniform of sex is not  well from 
40 to 55 and from 56
 to
>> >> 71. I did the correlation analysis between age and volume. I don't know 
how I can explain this
>> >> problem. 
>> >>   Thanks again.
>> >> 
>> >> Sincerely,

>> >> Zheng  
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:

>> >> >Hi Zheng
>> >> >
>> >> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >> >wouldn't expect very large effects until you get into the older end of 
>> >> >that range. Have you scatter plotted your data?

>> >> >Bruce
>> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >wrote:

>> >> >
>> >> >> 
>> >> >> Hi Bruce,
>> >> >> 
>> >> >>     Thank you for your help.

>> >> >>     I have  54 subjects, aged from 21 to 71 and only one group. I want 
to compare the chang
e o
>> f
>> >> >> hippocampus volume with age. The results before and after doing the 
correction for eTIV are
 th
>> e
>> >> >> same. Where is wrong? Or if there is no error, how can I explain it in 
discussion?
>> >> >> 
>> >> >> Thanks,

>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:

>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >yes, I see. Maybe the effect is smaller than you have the power to see, or 
>> >> >> >there is no effect? You would need to give us more details for us to help. 
>> >> >> >Are you correcting for eTIV? What measure are you comparing?

>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi Bruce,
>> >> >> >> 
>> >> >> >>      I am sorry for this situation. 

>> >> >> >>      In the first way, there was an statistical difference in left 
hippocampus, but no d
iff
>> ere
>> >> nce
>> >> >>  in
>> >> >> >> right hippocampus. In the second way, there was both no statistical 
difference in left o
r
>> >> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >> >>      Can you understand me this time?
>> >> >> >> 
>> >> >> >> Thanks,

>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:

>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >no difference between what and what?
>> >> >> >> >
>> >> >> >> >cheers
>> >> >> >> >Bruce
>> >> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >
>> >> >> >> >> Hi professor,
>> >> >> >> >> 
>> >> >> >> >>     I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> >> >> >> got the result that there w

>> >> >> >> as
>> >> >> >> >> an obvious difference in left hippocampus, but no difference in 
right hippocampus. Th
en,
>>  I 
>> >> run

>> >> >> >> >> segmentation of hippocampus subfields. The result showed there 
is no difference in to
tal
>>  le
>> >> ft 
>> >> >> or

>> >> >> >> >> right hippocampus, and only in two right hippocampus subfields 
has significant differ
enc
>> e. 
>> >> Why
>> >> >>  is
>> >> >> >> >> there inconsistent result in two means? 
>> >> >> >> >>     Thank you very much.
>> >> >> >> >> 
>> >> >> >> >> Sincerely,

>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >>  
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >>
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >>  
>> >> >> >> 
>> >> >> >> 
>> >> >> >>
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>




 

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


 Thanks for your quick reply. These results are not correted by eTIV, If 
eTIV are corrected, I can only get the p value and scatter plot, I can't get 
the line trend. Do you know how to get the line trend with eTIV corrected as 
these results?


Thanks,
Zheng 








在 2017-11-22 10:14:16，"Bruce Fischl"  写道：
>is this eTIV corrected? I would look at some of the outliers and make 
>sure that the segmentations are accurate. Certainly the trend is in the 
>correct (and depressing) direction.
>
>cheers
>Bruce
>On Wed, 22 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>> Thanks for your advice. There are a part of the result. Blue color 
>> stands women, and Red color
>> stands men.
>> The number of the data is not enough large. Are they ok? May I use them 
>> in my paper?
>> [IMAGE][IMAGE][IMAGE]
>> 
>> 
>> Thanks a lot !
>> Zheng
>> 
>> 
>> 
>> 
>> At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:
>> >Hi Zheng
>> >
>> >I would scatter plot age vs. volume, coloring men and women differently 
>> >(or different symbols) with and without eTIV correction to get an idea of 
>> >what is going on
>> >
>> >cheers
>> >Bruce
>> >
>> >
>> >On Mon, 20 Nov 
>> >2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >>  
>> >>   My data is loss from 35 to 40. But the uniform of sex is not  well from 
>> >> 40 to 55 and from 56 to
>> >> 71. I did the correlation analysis between age and volume. I don't know 
>> >> how I can explain this
>> >> problem. 
>> >>   Thanks again.
>> >> 
>> >> Sincerely,
>> >> Zheng  
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:
>> >> >Hi Zheng
>> >> >
>> >> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >> >wouldn't expect very large effects until you get into the older end of 
>> >> >that range. Have you scatter plotted your data?
>> >> >Bruce
>> >> >On Mon, 20 Nov 2017, 郑凤莲 
>> >> >wrote:
>> >> >
>> >> >> 
>> >> >> Hi Bruce,
>> >> >> 
>> >> >> Thank you for your help.
>> >> >> I have  54 subjects, aged from 21 to 71 and only one group. I want 
>> >> >> to compare the change o
>> f
>> >> >> hippocampus volume with age. The results before and after doing the 
>> >> >> correction for eTIV are th
>> e
>> >> >> same. Where is wrong? Or if there is no error, how can I explain it in 
>> >> >> discussion?
>> >> >> 
>> >> >> Thanks,
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-20 04:55:49, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >yes, I see. Maybe the effect is smaller than you have the power to 
>> >> >> >see, or 
>> >> >> >there is no effect? You would need to give us more details for us to 
>> >> >> >help. 
>> >> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi Bruce,
>> >> >> >> 
>> >> >> >>  I am sorry for this situation. 
>> >> >> >>  In the first way, there was an statistical difference in left 
>> >> >> >> hippocampus, but no diff
>> ere
>> >> nce
>> >> >>  in
>> >> >> >> right hippocampus. In the second way, there was both no statistical 
>> >> >> >> difference in left or
>> >> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >> >>  Can you understand me this time?
>> >> >> >> 
>> >> >> >> Thanks,
>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >> At 2017-11-18 22:58:56, "Bruce Fischl"  
>> >> >> >> wrote:
>> >> >> >> >Hi Zheng
>> >> >> >> >
>> >> >> >> >no difference between what and what?
>> >> >> >> >
>> >> >> >> >cheers
>> >> >> >> >Bruce
>> >> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >> >
>> >> >> >> >> Hi professor,
>> >> >> >> >> 
>> >> >> >> >> I am using Freesurfer for DTI data. When I run 
>> >> >> >> >> 'mri_segstats', I 
>> >> >> >> >> got the result that there w
>> >> >> >> as
>> >> >> >> >> an obvious difference in left hippocampus, but no difference in 
>> >> >> >> >> right hippocampus. Then,
>>  I 
>> >> run
>> >> >> >> >> segmentation of hippocampus subfields. The result showed there 
>> >> >> >> >> is no difference in total
>>  le
>> >> ft 
>> >> >> or
>> >> >> >> >> right hippocampus, and only in two right hippocampus subfields 
>> >> >> >> >> has significant differenc
>> e. 
>> >> Why
>> >> >>  is
>> >> >> >> >> there inconsistent result in two means? 
>> >> >> >> >> Thank you very much.
>> >> >> >> >> 
>> >> >> >> >> Sincerely,
>> >> >> >> >> Zheng
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >>  
>> >> >> >> >> 
>> >> >> >> >> 
>> >> >> >> >>
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >>  
>> >> >> >> 
>> >> >> >> 
>> >> >> >>
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  

Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

is this eTIV corrected? I would look at some of the outliers and make 
sure that the segmentations are accurate. Certainly the trend is in the 
correct (and depressing) direction.


cheers
Bruce
On Wed, 22 Nov 2017, 郑凤莲 wrote:


Hi Bruce,

    Thanks for your advice. There are a part of the result. Blue color stands 
women, and Red color
stands men.
    The number of the data is not enough large. Are they ok? May I use them in 
my paper?
[IMAGE][IMAGE][IMAGE]


Thanks a lot !
Zheng




At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:
>Hi Zheng
>
>I would scatter plot age vs. volume, coloring men and women differently 
>(or different symbols) with and without eTIV correction to get an idea of 
>what is going on

>
>cheers
>Bruce
>
>
>On Mon, 20 Nov 
>2017, 郑凤莲 wrote:

>
>> Hi Bruce,
>>  
>>   My data is loss from 35 to 40. But the uniform of sex is not  well from 40 
to 55 and from 56 to
>> 71. I did the correlation analysis between age and volume. I don't know how 
I can explain this
>> problem. 
>>   Thanks again.
>> 
>> Sincerely,

>> Zheng  
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:

>> >Hi Zheng
>> >
>> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >wouldn't expect very large effects until you get into the older end of 
>> >that range. Have you scatter plotted your data?

>> >Bruce
>> >On Mon, 20 Nov 2017, 郑凤莲 
>> >wrote:

>> >
>> >> 
>> >> Hi Bruce,
>> >> 
>> >>     Thank you for your help.

>> >>     I have  54 subjects, aged from 21 to 71 and only one group. I want to 
compare the change o
f
>> >> hippocampus volume with age. The results before and after doing the 
correction for eTIV are th
e
>> >> same. Where is wrong? Or if there is no error, how can I explain it in 
discussion?
>> >> 
>> >> Thanks,

>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:

>> >> >Hi Zheng
>> >> >
>> >> >yes, I see. Maybe the effect is smaller than you have the power to see, or 
>> >> >there is no effect? You would need to give us more details for us to help. 
>> >> >Are you correcting for eTIV? What measure are you comparing?

>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >> 
>> >> >>      I am sorry for this situation. 

>> >> >>      In the first way, there was an statistical difference in left 
hippocampus, but no diff
ere
>> nce
>> >>  in
>> >> >> right hippocampus. In the second way, there was both no statistical 
difference in left or
>> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >>      Can you understand me this time?
>> >> >> 
>> >> >> Thanks,

>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:

>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >no difference between what and what?
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi professor,
>> >> >> >> 
>> >> >> >>     I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> >> >> got the result that there w

>> >> >> as
>> >> >> >> an obvious difference in left hippocampus, but no difference in 
right hippocampus. Then,
 I 
>> run

>> >> >> >> segmentation of hippocampus subfields. The result showed there is 
no difference in total
 le
>> ft 
>> >> or

>> >> >> >> right hippocampus, and only in two right hippocampus subfields has 
significant differenc
e. 
>> Why
>> >>  is
>> >> >> >> there inconsistent result in two means? 
>> >> >> >>     Thank you very much.
>> >> >> >> 
>> >> >> >> Sincerely,

>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >>  
>> >> >> >> 
>> >> >> >> 
>> >> >> >>
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>




 


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Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


Thanks for your advice. There are a part of the result. Blue color stands 
women, and Red color stands men.
The number of the data is not enough large. Are they ok? May I use them in 
my paper?




Thanks a lot !
Zheng








At 2017-11-20 10:15:49, "Bruce Fischl"  wrote:
>Hi Zheng
>
>I would scatter plot age vs. volume, coloring men and women differently 
>(or different symbols) with and without eTIV correction to get an idea of 
>what is going on
>
>cheers
>Bruce
>
>
>On Mon, 20 Nov 
>2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>>  
>>   My data is loss from 35 to 40. But the uniform of sex is not  well from 40 
>> to 55 and from 56 to
>> 71. I did the correlation analysis between age and volume. I don't know how 
>> I can explain this
>> problem. 
>>   Thanks again.
>> 
>> Sincerely,
>> Zheng  
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:
>> >Hi Zheng
>> >
>> >how uniform is your distribution? I'm hardly an expert on this, but I 
>> >wouldn't expect very large effects until you get into the older end of 
>> >that range. Have you scatter plotted your data?
>> >Bruce
>> >On Mon, 20 Nov 2017, 郑凤莲 
>> >wrote:
>> >
>> >> 
>> >> Hi Bruce,
>> >> 
>> >> Thank you for your help.
>> >> I have  54 subjects, aged from 21 to 71 and only one group. I want to 
>> >> compare the change of
>> >> hippocampus volume with age. The results before and after doing the 
>> >> correction for eTIV are the
>> >> same. Where is wrong? Or if there is no error, how can I explain it in 
>> >> discussion?
>> >> 
>> >> Thanks,
>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:
>> >> >Hi Zheng
>> >> >
>> >> >yes, I see. Maybe the effect is smaller than you have the power to see, 
>> >> >or 
>> >> >there is no effect? You would need to give us more details for us to 
>> >> >help. 
>> >> >Are you correcting for eTIV? What measure are you comparing?
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi Bruce,
>> >> >> 
>> >> >>  I am sorry for this situation. 
>> >> >>  In the first way, there was an statistical difference in left 
>> >> >> hippocampus, but no differe
>> nce
>> >>  in
>> >> >> right hippocampus. In the second way, there was both no statistical 
>> >> >> difference in left or
>> >> >> right  hippocampus. I don't know what causes this result. 
>> >> >>  Can you understand me this time?
>> >> >> 
>> >> >> Thanks,
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >> At 2017-11-18 22:58:56, "Bruce Fischl"  
>> >> >> wrote:
>> >> >> >Hi Zheng
>> >> >> >
>> >> >> >no difference between what and what?
>> >> >> >
>> >> >> >cheers
>> >> >> >Bruce
>> >> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >> >
>> >> >> >> Hi professor,
>> >> >> >> 
>> >> >> >> I am using Freesurfer for DTI data. When I run 'mri_segstats', 
>> >> >> >> I 
>> >> >> >> got the result that there w
>> >> >> as
>> >> >> >> an obvious difference in left hippocampus, but no difference in 
>> >> >> >> right hippocampus. Then, I 
>> run
>> >> >> >> segmentation of hippocampus subfields. The result showed there is 
>> >> >> >> no difference in total le
>> ft 
>> >> or
>> >> >> >> right hippocampus, and only in two right hippocampus subfields has 
>> >> >> >> significant difference. 
>> Why
>> >>  is
>> >> >> >> there inconsistent result in two means? 
>> >> >> >> Thank you very much.
>> >> >> >> 
>> >> >> >> Sincerely,
>> >> >> >> Zheng
>> >> >> >> 
>> >> >> >> 
>> >> >> >> 
>> >> >> >>  
>> >> >> >> 
>> >> >> >> 
>> >> >> >>
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>
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Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

Hi Zheng

I would scatter plot age vs. volume, coloring men and women differently 
(or different symbols) with and without eTIV correction to get an idea of 
what is going on


cheers
Bruce


On Mon, 20 Nov 
2017, 郑凤莲 wrote:



Hi Bruce,
 
  My data is loss from 35 to 40. But the uniform of sex is not  well from 40 to 
55 and from 56 to
71. I did the correlation analysis between age and volume. I don't know how I 
can explain this
problem. 
  Thanks again.

Sincerely,
Zheng  





At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:
>Hi Zheng
>
>how uniform is your distribution? I'm hardly an expert on this, but I 
>wouldn't expect very large effects until you get into the older end of 
>that range. Have you scatter plotted your data?

>Bruce
>On Mon, 20 Nov 2017, 郑凤莲 
>wrote:

>
>> 
>> Hi Bruce,
>> 
>>     Thank you for your help.

>>     I have  54 subjects, aged from 21 to 71 and only one group. I want to 
compare the change of
>> hippocampus volume with age. The results before and after doing the 
correction for eTIV are the
>> same. Where is wrong? Or if there is no error, how can I explain it in 
discussion?
>> 
>> Thanks,

>> Zheng
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:

>> >Hi Zheng
>> >
>> >yes, I see. Maybe the effect is smaller than you have the power to see, or 
>> >there is no effect? You would need to give us more details for us to help. 
>> >Are you correcting for eTIV? What measure are you comparing?

>> >
>> >cheers
>> >Bruce
>> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>      I am sorry for this situation. 

>> >>      In the first way, there was an statistical difference in left 
hippocampus, but no differe
nce
>>  in
>> >> right hippocampus. In the second way, there was both no statistical 
difference in left or
>> >> right  hippocampus. I don't know what causes this result. 
>> >>      Can you understand me this time?
>> >> 
>> >> Thanks,

>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:

>> >> >Hi Zheng
>> >> >
>> >> >no difference between what and what?
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi professor,
>> >> >> 
>> >> >>     I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> >> got the result that there w

>> >> as
>> >> >> an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I 
run

>> >> >> segmentation of hippocampus subfields. The result showed there is no 
difference in total le
ft 
>> or

>> >> >> right hippocampus, and only in two right hippocampus subfields has 
significant difference. 
Why
>>  is
>> >> >> there inconsistent result in two means? 
>> >> >>     Thank you very much.
>> >> >> 
>> >> >> Sincerely,

>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>




 


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Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,
 
  My data is loss from 35 to 40. But the uniform of sex is not  well from 40 to 
55 and from 56 to 71. I did the correlation analysis between age and volume. I 
don't know how I can explain this problem. 
  Thanks again.


Sincerely,
Zheng  








At 2017-11-20 09:35:45, "Bruce Fischl"  wrote:
>Hi Zheng
>
>how uniform is your distribution? I'm hardly an expert on this, but I 
>wouldn't expect very large effects until you get into the older end of 
>that range. Have you scatter plotted your data?
>Bruce
>On Mon, 20 Nov 2017, 郑凤莲 
>wrote:
>
>> 
>> Hi Bruce,
>> 
>> Thank you for your help.
>> I have  54 subjects, aged from 21 to 71 and only one group. I want to 
>> compare the change of
>> hippocampus volume with age. The results before and after doing the 
>> correction for eTIV are the
>> same. Where is wrong? Or if there is no error, how can I explain it in 
>> discussion?
>> 
>> Thanks,
>> Zheng
>> 
>> 
>> 
>> 
>> 
>> At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:
>> >Hi Zheng
>> >
>> >yes, I see. Maybe the effect is smaller than you have the power to see, or 
>> >there is no effect? You would need to give us more details for us to help. 
>> >Are you correcting for eTIV? What measure are you comparing?
>> >
>> >cheers
>> >Bruce
>> >  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi Bruce,
>> >> 
>> >>  I am sorry for this situation. 
>> >>  In the first way, there was an statistical difference in left 
>> >> hippocampus, but no difference
>>  in
>> >> right hippocampus. In the second way, there was both no statistical 
>> >> difference in left or
>> >> right  hippocampus. I don't know what causes this result. 
>> >>  Can you understand me this time?
>> >> 
>> >> Thanks,
>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >> 
>> >> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:
>> >> >Hi Zheng
>> >> >
>> >> >no difference between what and what?
>> >> >
>> >> >cheers
>> >> >Bruce
>> >> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >> >
>> >> >> Hi professor,
>> >> >> 
>> >> >> I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> >> got the result that there w
>> >> as
>> >> >> an obvious difference in left hippocampus, but no difference in right 
>> >> >> hippocampus. Then, I run
>> >> >> segmentation of hippocampus subfields. The result showed there is no 
>> >> >> difference in total left 
>> or
>> >> >> right hippocampus, and only in two right hippocampus subfields has 
>> >> >> significant difference. Why
>>  is
>> >> >> there inconsistent result in two means? 
>> >> >> Thank you very much.
>> >> >> 
>> >> >> Sincerely,
>> >> >> Zheng
>> >> >> 
>> >> >> 
>> >> >> 
>> >> >>  
>> >> >> 
>> >> >> 
>> >> >>
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>
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Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

Hi Zheng

how uniform is your distribution? I'm hardly an expert on this, but I 
wouldn't expect very large effects until you get into the older end of 
that range. Have you scatter plotted your data?

Bruce
On Mon, 20 Nov 2017, 郑凤莲 
wrote:




Hi Bruce,

    Thank you for your help.
    I have  54 subjects, aged from 21 to 71 and only one group. I want to 
compare the change of
hippocampus volume with age. The results before and after doing the correction 
for eTIV are the
same. Where is wrong? Or if there is no error, how can I explain it in 
discussion?

Thanks,
Zheng





At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:
>Hi Zheng
>
>yes, I see. Maybe the effect is smaller than you have the power to see, or 
>there is no effect? You would need to give us more details for us to help. 
>Are you correcting for eTIV? What measure are you comparing?

>
>cheers
>Bruce
>  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>>      I am sorry for this situation. 

>>      In the first way, there was an statistical difference in left 
hippocampus, but no difference
 in
>> right hippocampus. In the second way, there was both no statistical 
difference in left or
>> right  hippocampus. I don't know what causes this result. 
>>      Can you understand me this time?
>> 
>> Thanks,

>> Zheng
>> 
>> 
>> 
>> 
>> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:

>> >Hi Zheng
>> >
>> >no difference between what and what?
>> >
>> >cheers
>> >Bruce
>> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi professor,
>> >> 
>> >>     I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> got the result that there w

>> as
>> >> an obvious difference in left hippocampus, but no difference in right 
hippocampus. Then, I run
>> >> segmentation of hippocampus subfields. The result showed there is no difference in total left 
or

>> >> right hippocampus, and only in two right hippocampus subfields has 
significant difference. Why
 is
>> >> there inconsistent result in two means? 
>> >>     Thank you very much.
>> >> 
>> >> Sincerely,

>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>




 


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Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


Thank you for your help.
I have  54 subjects, aged from 21 to 71 and only one group. I want to 
compare the change of hippocampus volume with age. The results before and after 
doing the correction for eTIV are the same. Where is wrong? Or if there is no 
error, how can I explain it in discussion?


Thanks,
Zheng








At 2017-11-20 04:55:49, "Bruce Fischl"  wrote:
>Hi Zheng
>
>yes, I see. Maybe the effect is smaller than you have the power to see, or 
>there is no effect? You would need to give us more details for us to help. 
>Are you correcting for eTIV? What measure are you comparing?
>
>cheers
>Bruce
>  On Sun, 19 Nov 2017, 郑凤莲 wrote:
>
>> Hi Bruce,
>> 
>>  I am sorry for this situation. 
>>  In the first way, there was an statistical difference in left 
>> hippocampus, but no difference in
>> right hippocampus. In the second way, there was both no statistical 
>> difference in left or
>> right  hippocampus. I don't know what causes this result. 
>>  Can you understand me this time?
>> 
>> Thanks,
>> Zheng
>> 
>> 
>> 
>> 
>> At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:
>> >Hi Zheng
>> >
>> >no difference between what and what?
>> >
>> >cheers
>> >Bruce
>> >On Fri, 17 Nov 2017, 郑凤莲 wrote:
>> >
>> >> Hi professor,
>> >> 
>> >> I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> >> got the result that there w
>> as
>> >> an obvious difference in left hippocampus, but no difference in right 
>> >> hippocampus. Then, I run
>> >> segmentation of hippocampus subfields. The result showed there is no 
>> >> difference in total left or
>> >> right hippocampus, and only in two right hippocampus subfields has 
>> >> significant difference. Why is
>> >> there inconsistent result in two means? 
>> >> Thank you very much.
>> >> 
>> >> Sincerely,
>> >> Zheng
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>> 
>>  
>> 
>> 
>>
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Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

Hi Zheng

yes, I see. Maybe the effect is smaller than you have the power to see, or 
there is no effect? You would need to give us more details for us to help. 
Are you correcting for eTIV? What measure are you comparing?


cheers
Bruce
 On Sun, 19 Nov 2017, 郑凤莲 wrote:


Hi Bruce,

     I am sorry for this situation. 
     In the first way, there was an statistical difference in left hippocampus, 
but no difference in
right hippocampus. In the second way, there was both no statistical difference 
in left or
right  hippocampus. I don't know what causes this result. 
     Can you understand me this time?

Thanks,
Zheng




At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:
>Hi Zheng
>
>no difference between what and what?
>
>cheers
>Bruce
>On Fri, 17 Nov 2017, 郑凤莲 wrote:
>
>> Hi professor,
>> 
>>     I am using Freesurfer for DTI data. When I run 'mri_segstats', I 
>> got the result that there w

as
>> an obvious difference in left hippocampus, but no difference in right 
hippocampus. Then, I run
>> segmentation of hippocampus subfields. The result showed there is no 
difference in total left or
>> right hippocampus, and only in two right hippocampus subfields has 
significant difference. Why is
>> there inconsistent result in two means? 
>>     Thank you very much.
>> 
>> Sincerely,

>> Zheng
>> 
>> 
>> 
>>  
>> 
>> 
>>




 


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Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Bruce,


 I am sorry for this situation. 
 In the first way, there was an statistical difference in left hippocampus, 
but no difference in right hippocampus. In the second way, there was both no 
statistical difference in left or right  hippocampus. I don't know what causes 
this result. 
 Can you understand me this time?



Thanks,
Zheng







At 2017-11-18 22:58:56, "Bruce Fischl"  wrote:
>Hi Zheng
>
>no difference between what and what?
>
>cheers
>Bruce
>On Fri, 17 Nov 2017, 郑凤莲 wrote:
>
>> Hi professor,
>> 
>> I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got 
>> the result that there was
>> an obvious difference in left hippocampus, but no difference in right 
>> hippocampus. Then, I run
>> segmentation of hippocampus subfields. The result showed there is no 
>> difference in total left or
>> right hippocampus, and only in two right hippocampus subfields has 
>> significant difference. Why is
>> there inconsistent result in two means? 
>> Thank you very much.
>> 
>> Sincerely,
>> Zheng
>> 
>> 
>> 
>>  
>> 
>> 
>>
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Re: [Freesurfer] hippocampus subfields

[Bruce Fischl]

Hi Zheng

no difference between what and what?

cheers
Bruce
On Fri, 17 Nov 2017, 郑凤莲 wrote:


Hi professor,

    I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was
an obvious difference in left hippocampus, but no difference in right 
hippocampus. Then, I run
segmentation of hippocampus subfields. The result showed there is no difference 
in total left or
right hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is
there inconsistent result in two means? 
    Thank you very much.

Sincerely,
Zheng



 


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Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Hi Eugenio,


Thank you very much.
I have 54 subjects, aged from 21 to 71. I ran 'recon-all -all' and 
'recon-all -qcache', and acquired the volume of  hippocampus from the 
aseg.stats. Then I used SPSS to calculate correlation between age and volume 
without  correcting by intracranial volume. For hippocampus subfields, I also 
did it without  correcting by intracranial volume. 

Thanks,
Zheng







At 2017-11-17 21:40:20, "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> 
wrote:


Hi again, Zheng,

How many subjects do you have? Did you correct by intracranial volume? What is 
the age range?

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 17 November 2017 at 12:41
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] hippocampus subfields

 

Dear Eugenio,

 

 Thank you for your reply. I  am sorry that I don't express it clearly.

 FIrstly, I ran egstats2label --subjects subjid --meas volume --segno 17 53 
--tablefile $SUBJECTS_DIR/ASEGSTATS.txt' and acquired the volume value of left 
and right hippocampus. Then I used SPSS software to calculate the relationship 
between volume and age, the P value in the left is 0.029 and the right is 
0.125. It showed that there is difference in volume of the left  hippocampus, 
but the right isn't. 

 Secondly, I ran 'recon-all -s subjid -all -hippocampal-subfields-T1', and 
get the volume of hippocampus subfields. The p value of left_whole_hippocampus 
is 0.229 and the right is 0.468. There is no difference in left or right 
hippocampus.

 My doubt is that why there is an obvious difference between the results of 
two ways. Can I speak in this way? If it still not clear, please tell me what 
you need, I will provide it for you.

 

Thanks,

Zheng 







At 2017-11-17 17:54:13, "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> 
wrote:



Dear Zheng,

Do you think you could provide us with some more detail on your analyses?

Cheers,

/Eugenio

 

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 17 November 2017 at 09:40
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampus subfields

 

Hi professor,

I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was anobvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of  hippocampus 
subfields. The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means? 
Thank you very much.

Sincerely,
Zheng











 ___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] hippocampus subfields

[Iglesias Gonzalez, Eugenio]

Hi again, Zheng,
How many subjects do you have? Did you correct by intracranial volume? What is 
the age range?

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 17 November 2017 at 12:41
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] hippocampus subfields

Dear Eugenio,

 Thank you for your reply. I  am sorry that I don't express it clearly.
 FIrstly, I ran egstats2label --subjects subjid --meas volume --segno 17 53 
--tablefile $SUBJECTS_DIR/ASEGSTATS.txt' and acquired the volume value of left 
and right hippocampus. Then I used SPSS software to calculate the relationship 
between volume and age, the P value in the left is 0.029 and the right is 
0.125. It showed that there is difference in volume of the left  hippocampus, 
but the right isn't.
 Secondly, I ran 'recon-all -s subjid -all -hippocampal-subfields-T1', and 
get the volume of hippocampus subfields. The p value of left_whole_hippocampus 
is 0.229 and the right is 0.468. There is no difference in left or right 
hippocampus.
 My doubt is that why there is an obvious difference between the results of 
two ways. Can I speak in this way? If it still not clear, please tell me what 
you need, I will provide it for you.

Thanks,
Zheng




At 2017-11-17 17:54:13, "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> 
wrote:

Dear Zheng,
Do you think you could provide us with some more detail on your analyses?
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 郑凤莲 <13181786...@163.com<mailto:13181786...@163.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 17 November 2017 at 09:40
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] hippocampus subfields

Hi professor,

I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was anobvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of  hippocampus 
subfields. The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means?
Thank you very much.

Sincerely,
Zheng








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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampus subfields

[郑凤莲]

Dear Eugenio,


 Thank you for your reply. I  am sorry that I don't express it clearly.
 FIrstly, I ran egstats2label --subjects subjid --meas volume --segno 17 53 
--tablefile $SUBJECTS_DIR/ASEGSTATS.txt' and acquired the volume value of left 
and right hippocampus. Then I used SPSS software to calculate the relationship 
between volume and age, the P value in the left is 0.029 and the right is 
0.125. It showed that there is difference in volume of the left  hippocampus, 
but the right isn't. 
 Secondly, I ran 'recon-all -s subjid -all -hippocampal-subfields-T1', and 
get the volume of hippocampus subfields. The p value of left_whole_hippocampus 
is 0.229 and the right is 0.468. There is no difference in left or right 
hippocampus.
 My doubt is that why there is an obvious difference between the results of 
two ways. Can I speak in this way? If it still not clear, please tell me what 
you need, I will provide it for you.


Thanks,
Zheng 







At 2017-11-17 17:54:13, "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> 
wrote:


Dear Zheng,

Do you think you could provide us with some more detail on your analyses?

Cheers,

/Eugenio

 

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 17 November 2017 at 09:40
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampus subfields

 

Hi professor,

I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was anobvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of  hippocampus 
subfields.The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means? 
Thank you very much.

Sincerely,
Zheng


___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampus subfields

[Iglesias Gonzalez, Eugenio]

Dear Zheng,
Do you think you could provide us with some more detail on your analyses?
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 17 November 2017 at 09:40
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampus subfields

Hi professor,

I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was anobvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of  hippocampus 
subfields. The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means?
Thank you very much.

Sincerely,
Zheng


___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] hippocampus subfields

[郑凤莲]

Hi professor,

I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was anobvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of  hippocampus 
subfields.The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means? 
Thank you very much.

Sincerely,
Zheng



___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] hippocampus subfields

[郑凤莲]

Hi professor,


I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the 
result that there was an obvious difference in left hippocampus, but no 
difference in right hippocampus. Then, I run segmentation of hippocampus 
subfields. The result showed there is no difference in total left or right 
hippocampus, and only in two right hippocampus subfields has significant 
difference. Why is there inconsistent result in two means? 
Thank you very much.


Sincerely,
Zheng___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampus subfields in longitudinal dataset

[Iglesias Gonzalez, Eugenio]

Yes, no problem! As long as you explain it in any publication that might come 
out of these analyses.
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 18/09/2017, 14:43, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lara 
Foland-Ross" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
lfol...@stanford.edu> wrote:

Thank you! A quick followup question:

I'm interested in running the new devel version (e.g., segmentHA_T1_long.sh 
from 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
 on my data which was originally processed using the longitudinal pipeline in 
version 5.3. 

Can you please confirm that this is appropriate?

Thanks,
Lara

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, 
Eugenio <e.igles...@ucl.ac.uk>
Sent: Thursday, September 14, 2017 12:12 PM
To: Freesurfer support list
    Subject: Re: [Freesurfer] hippocampus subfields in longitudinal dataset

Dear Lara,
The sh script implements a longitudinal segmentation algorithm that 
segments both time points simultaneously using a subject specific atlas, 
improving the reliability of the segmentation. You can read the details here
http://www.sciencedirect.com/science/article/pii/S1053811916303275
Cheers
Eugenio


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross 
<lfol...@stanford.edu>
Sent: Thursday, September 14, 2017 2:38:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] hippocampus subfields in longitudinal dataset

Hello Freesurfer experts,

I have a longitudinal data set already processed in the longitudinal 
pipeline of v5.3. I'd now like to use the hippocampus subfield commands 
available in 6.0.

I'm wondering whether I will arrive at the same result using either of the 
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the 
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh

Thanks in advance,
Lara



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender and 
properly
dispose of the e-mail.



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___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] hippocampus subfields in longitudinal dataset

[Lara Foland-Ross]

Thank you! A quick followup question:

I'm interested in running the new devel version (e.g., segmentHA_T1_long.sh 
from 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
 on my data which was originally processed using the longitudinal pipeline in 
version 5.3. 

Can you please confirm that this is appropriate?

Thanks,
Lara

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, 
Eugenio <e.igles...@ucl.ac.uk>
Sent: Thursday, September 14, 2017 12:12 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields in longitudinal dataset

Dear Lara,
The sh script implements a longitudinal segmentation algorithm that segments 
both time points simultaneously using a subject specific atlas, improving the 
reliability of the segmentation. You can read the details here
http://www.sciencedirect.com/science/article/pii/S1053811916303275
Cheers
Eugenio


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross 
<lfol...@stanford.edu>
Sent: Thursday, September 14, 2017 2:38:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] hippocampus subfields in longitudinal dataset

Hello Freesurfer experts,

I have a longitudinal data set already processed in the longitudinal pipeline 
of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0.

I'm wondering whether I will arrive at the same result using either of the 
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the 
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh

Thanks in advance,
Lara



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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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Re: [Freesurfer] hippocampus subfields in longitudinal dataset

[Iglesias Gonzalez, Eugenio]

Dear Lara,
The sh script implements a longitudinal segmentation algorithm that segments 
both time points simultaneously using a subject specific atlas, improving the 
reliability of the segmentation. You can read the details here
http://www.sciencedirect.com/science/article/pii/S1053811916303275
Cheers
Eugenio


Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross 
<lfol...@stanford.edu>
Sent: Thursday, September 14, 2017 2:38:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] hippocampus subfields in longitudinal dataset

Hello Freesurfer experts,

I have a longitudinal data set already processed in the longitudinal pipeline 
of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0.

I'm wondering whether I will arrive at the same result using either of the 
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the 
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh

Thanks in advance,
Lara



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but does not contain patient information, please contact the sender and properly
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] hippocampus subfields in longitudinal dataset

[Lara Foland-Ross]

Hello Freesurfer experts,

I have a longitudinal data set already processed in the longitudinal pipeline 
of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0.

I'm wondering whether I will arrive at the same result using either of the 
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the 
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh

Thanks in advance,
Lara



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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampus subfields

[Kanel, Prabesh]

Sweet, just what I wanted.


Thank you,


Prabesh




From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias 
<e.igles...@bcbl.eu>
Sent: Wednesday, March 2, 2016 2:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

OK now I get it ;-)
You can simply do:
mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl 
[lr]h.hippoSfLabels-T1-T2.v10.mgz
The rl flag says: "reslice like the following volume"
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" <pk...@my.fsu.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 2, 2016 8:31:17 PM
Subject: Re: [Freesurfer] hippocampus subfields



Hi Eugenio,


Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points.


Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location?


Best Regards,

Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias 
<e.igles...@bcbl.eu>
Sent: Wednesday, March 2, 2016 12:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

Hi Prabesh,
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data.
Regarding your second question: I'm sure it's not too trivial ;-)  but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space?
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" <pk...@my.fsu.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 2, 2016 6:07:13 PM
Subject: [Freesurfer] hippocampus subfields


Freesurfer List,


I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further.  That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email.

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial.

Regards,

Prabesh

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Re: [Freesurfer] hippocampus subfields

[Eugenio Iglesias]

OK now I get it ;-) 
You can simply do: 
mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl 
[lr]h.hippoSfLabels-T1-T2.v10.mgz 
The rl flag says: "reslice like the following volume" 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel" <pk...@my.fsu.edu> 
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Sent: Wednesday, March 2, 2016 8:31:17 PM 
Subject: Re: [Freesurfer] hippocampus subfields 




Hi Eugenio, 



Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points. 



Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location? 


Best Regards, 

Prabesh 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias 
<e.igles...@bcbl.eu> 
Sent: Wednesday, March 2, 2016 12:23 PM 
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampus subfields 
Hi Prabesh, 
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data. 
Regarding your second question: I'm sure it's not too trivial ;-) but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel" <pk...@my.fsu.edu> 
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Sent: Wednesday, March 2, 2016 6:07:13 PM 
Subject: [Freesurfer] hippocampus subfields 



Freesurfer List, 





I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further. That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email. 

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial. 

Regards, 

Prabesh 

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but does not contain patient information, please contact the sender and 
properly 
dispose of the e-mail. 

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Re: [Freesurfer] hippocampus subfields

[Kanel, Prabesh]

Hi Eugenio,


Thank you, for your quick reply. It has happened to me in 4% of the cases, but 
my data sample is small like 100 data points.


Addition to the second question: When I segment the hippocampus, I get the 
discrete segmentation volume at 0.333 mm resolution in the file 
[lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each 
voxel is labelled based on the subfield. I can use mri_extract_label or 
mri_binarize to extract individual subfield. But this segmentation will have 
voxels with the original label. If I load the file along with the 
T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the 
intensities at this place, I believe the intensity value is from 
T2.FSspace.mgz. Are those intensities values different from the original T2 
images? If not, Is it possible to get those value at each voxel location?


Best Regards,

Prabesh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias 
<e.igles...@bcbl.eu>
Sent: Wednesday, March 2, 2016 12:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields

Hi Prabesh,
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data.
Regarding your second question: I'm sure it's not too trivial ;-)  but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space?
Cheers,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Prabesh Kanel" <pk...@my.fsu.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 2, 2016 6:07:13 PM
Subject: [Freesurfer] hippocampus subfields


Freesurfer List,


I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further.  That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email.

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial.

Regards,

Prabesh

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampus subfields

[Eugenio Iglesias]

Hi Prabesh, 
I think this is due to a bug that I found recently and which I'm trying to 
track down. Has it happened to you with many scans? The failure rate is less 
than 1% in my data. 
Regarding your second question: I'm sure it's not too trivial ;-) but I don't 
understand exactly what you mean. Do you want to deform the segmentations back 
to the original T2 space? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Prabesh Kanel" <pk...@my.fsu.edu> 
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Sent: Wednesday, March 2, 2016 6:07:13 PM 
Subject: [Freesurfer] hippocampus subfields 



Freesurfer List, 





I ran recon-all to segment hippocampus subfield using the development version 
of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and 
T2 images. But for some of the scans, the process stops at a point and doesn't 
seem to progress further. That happens in only a few cases and only when the 
data are run using the flag -hippocampal-subfields-T1T2. I have attached a log 
file of one of the case in this email. 

Another query that I have is to get T2 segmented subfields images (one with 
intensity values rather than labels). Is there an easier way to get T2 
subfields segmented images using the segmentation volumes and T2.FSspace.mgz. 
Sorry, if this question seems too trivial. 

Regards, 

Prabesh 

___ 
Freesurfer mailing list 
Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 


The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at 
http://www.partners.org/complianceline . If the e-mail was sent to you in error 
but does not contain patient information, please contact the sender and 
properly 
dispose of the e-mail. 
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.