subject:"Re\: \[Freesurfer\] sclimbic sometimes does not detect left basal forebrain"

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-09-13 Thread Miriam Taza

External Email - Use Caution

Hello,
Im wondering if there is an update regarding etiv differences between recon all 
and using sclimbic. I want to divide the volumes extracted from using sclimbic 
on t1s by etiv.  Im not sure given the discrepancy if I should use etiv 
extracted from recon all command or from sclimbic.
Thanks,
Miriam

From: Miriam Taza 
Sent: Thursday, August 11, 2022 6:01 PM
To: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Hello,
I just wanted to follow up about etiv, if you had the chance to look into if 
your recon all vs sclimbic also does simithing similar on the subjs i sent?
I am also attaching another graph that depicts the difference between etivs 
extracted from sclimbic and from recon all.
[cid:89abfbda-77b0-4a5c-ade3-c4d18cc274d6]
Thanks for all your help,
Miriam

From: Miriam Taza 
Sent: Wednesday, August 3, 2022 4:59 PM
To: Douglas N. Greve 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Hello,

Attached are a few subjects, where YA denotes younger adults and OA older 
adults. I also included the stats file when I run sclimbic for reference. 
Please let me know if this mode of transfer works.

Thank you,
Miriam

P.S. I also sent a previous email regarding etiv values "etiv value differs if 
using recon all vs freesurfer dev". Are you able to also see if your sclimbic 
etiv values differ much from recon all? For example, sub1221084 etiv greatly 
differs between sclimbic, old recon all, and new recon all.




From: Douglas N. Greve 
Sent: Friday, July 29, 2022 12:29 PM
To: Miriam Taza 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

yes, you can try sending it to me. if they are too big for email, then we have 
other solutions

On 7/29/2022 12:19 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
Thank you for your quick response!
I can certainly share a few participants data with you but I would prefer not 
to share with the entire mailing list if possible. If so, should I attach it to 
this email?

I could send you more than one if you prefer.

Thank you,
Miriam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 29, 2022 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Can you send us a sample case?

On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam



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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-31 Thread Douglas N. Greve

I'm not sure but I have a guess. EAch stage of the unet has an intensity 
normalization step where the intensity of all voxels are spread 
uniformly over a range. I suspect that the bright, meaningless voxels 
are causing the meaningful voxels to be forced into too small of a range 
causing information loss.


On 8/31/2022 11:19 AM, Miriam Taza wrote:


External Email - Use Caution

thank you!
One last question hopefully on this matter. I dont fully understand 
still why the percentile flag would affect the subcortical regions? 
the bias field was only in the front and back of the brain.


Thanks,
Miriam

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


*Sent:* Sunday, August 28, 2022 4:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain



On 8/11/2022 6:02 PM, Miriam Taza wrote:


External Email - Use Caution

Hi again,

I have a few questions regarding this.

indeed it does appear that there is a bias field in all of these 
scans, but this is not specific to those that fail sclimbic.


 1. why do you think it is consistently *only* the *left* side that
fails? My question here is if whether it is mainly the left due
to the way sclimbic does its magic or if this might be due to the
actual data (i,e smaller left volumes might have an impact).

I have no idea. That's the problem with the machine learning stuff, it 
just gives you an answer without a reason.
2. I would really appreciate if someone could explain what 
--percentile 99.9 is doing a bit more as my results differ a lot 
depending if this flag is used or not.
Im asking because Im not sure what is the best input to use for 
sclimbic anymore
The --percentile 99.9 tells it to sort all the voxels by intensity. 
One of those voxels will rank the 99.9% in intensity. All voxels that 
are brighter than this intensity are then set to this intensity 
("clipping"). This represents more closely how ScLimbic was trained. I 
will make --percentile 99.9 the default on the next release.


I decided to look at differences(correlation) of volume (.stats) 
between sclimbic or sclimbic with --percentile 99.9 ran on T1s or on 
recon all results (I wanted to make confirm the results using recon 
all subj vs t1s with the percentile flag are similar given that recon 
all does correct for bias field).  below are the correlation and 
means. this was on subsample (n=180) and I only looked at one ROI.



left BF right BF
sclimbic x sclimbic99   0.480.62
sclimbic x recon99  0.300.55
sclimbic x recon0.300.55
recon99 x recon 0.990.99
recon99 x sclimbic990.910.95
recon x sclimbic99  0.920.95


avg left BF avg BF mean
sclimbic198.77  253.96
sclimbic99  297.99  328.93
recon   312.12  340.44
recon99 315.80  343.92


(recon = sclimbic ran on recon all outputs; recon99 = sclimbic 
--percentile 99 ran on recon outputs; sclimbic=ran sclimbic on t1s; 
sclimbic99=with flag ran on t1s)


*3.so the most important question is what would you judge to provide 
the "most accurate" result to be used in subsequent group analysis. 
recon99, recon, sclimbic, or sclimbic99.

*
*This confirms my suspicions above (ie, the training). The "recon" 
method will most closely track the training (and the results from the 
paper).*


Thank you very much!
Miriam

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miriam 
Taza  <mailto:miriam.t...@mail.mcgill.ca>

*Sent:* Wednesday, August 10, 2022 1:26 PM
*To:* Freesurfer support list  
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain


External Email - Use Caution

but this(bright at back and nose) also seems to be the case with 
participants that sclimbic did work on..



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

*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
There was something a little strange about the cases that were 
failing -- there were very bright values at the back of the head and 
around the nose. This probably messes up the normalization in the 
unet. I ran it wi

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-31 Thread Miriam Taza

External Email - Use Caution

thank you!
One last question hopefully on this matter. I dont fully understand still why 
the percentile flag would affect the subcortical regions? the bias field was 
only in the front and back of the brain.

Thanks,
Miriam

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

Sent: Sunday, August 28, 2022 4:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain



On 8/11/2022 6:02 PM, Miriam Taza wrote:

External Email - Use Caution

Hi again,

I have a few questions regarding this.

indeed it does appear that there is a bias field in all of these scans, but 
this is not specific to those that fail sclimbic.

  1.  why do you think it is consistently only the left side that fails? My 
question here is if whether it is mainly the left due to the way sclimbic does 
its magic or if this might be due to the actual data (i,e smaller left volumes 
might have an impact).

I have no idea. That's the problem with the machine learning stuff, it just 
gives you an answer without a reason.
2. I would really appreciate if someone could explain what --percentile 99.9 is 
doing a bit more as my results differ a lot depending if this flag is used or 
not.
Im asking because Im not sure what is the best input to use for sclimbic 
anymore
The --percentile 99.9 tells it to sort all the voxels by intensity. One of 
those voxels will rank the 99.9% in intensity. All voxels that are brighter 
than this intensity are then set to this intensity ("clipping"). This 
represents more closely how ScLimbic was trained. I will make --percentile 99.9 
the default on the next release.

I decided to look at differences(correlation) of volume (.stats) between 
sclimbic or sclimbic with --percentile 99.9 ran on T1s or on recon all results 
(I wanted to make confirm the results using recon all subj vs t1s with the 
percentile flag are similar given that recon all does correct for bias field).  
below are the correlation and means. this was on subsample (n=180) and I only 
looked at one ROI.


left BF right BF
sclimbic x sclimbic99   0.480.62
sclimbic x recon99  0.300.55
sclimbic x recon0.300.55
recon99 x recon 0.990.99
recon99 x sclimbic990.910.95
recon x sclimbic99  0.920.95


avg left BF avg BF mean
sclimbic198.77  253.96
sclimbic99  297.99  328.93
recon   312.12  340.44
recon99 315.80  343.92

(recon = sclimbic ran on recon all outputs; recon99 = sclimbic --percentile 99 
ran on recon outputs; sclimbic=ran sclimbic on t1s; sclimbic99=with flag ran on 
t1s)

3.so the most important question is what would you judge to provide the "most 
accurate" result to be used in subsequent group analysis. recon99, recon, 
sclimbic, or sclimbic99.
This confirms my suspicions above (ie, the training). The "recon" method will 
most closely track the training (and the results from the paper).

Thank you very much!
Miriam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Miriam Taza 
<mailto:miriam.t...@mail.mcgill.ca>
Sent: Wednesday, August 10, 2022 1:26 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain


External Email - Use Caution

but this(bright at back and nose) also seems to be the case with participants 
that sclimbic did work on..


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, August 9, 2022 10:34 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

There was something a little strange about the cases that were failing -- there 
were very bright values at the back of the head and around the nose. This 
probably messes up the normalization in the unet. I ran it with --percentile 
99.9 (this eliminates the extreme voxels) and the results looked ok after that.


On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-28 Thread Douglas N. Greve




On 8/11/2022 6:02 PM, Miriam Taza wrote:


External Email - Use Caution

Hi again,

I have a few questions regarding this.

indeed it does appear that there is a bias field in all of these 
scans, but this is not specific to those that fail sclimbic.


 1. why do you think it is consistently *only* the *left* side that
fails? My question here is if whether it is mainly the left due to
the way sclimbic does its magic or if this might be due to the
actual data (i,e smaller left volumes might have an impact).

I have no idea. That's the problem with the machine learning stuff, it 
just gives you an answer without a reason.
2. I would really appreciate if someone could explain what 
--percentile 99.9 is doing a bit more as my results differ a lot 
depending if this flag is used or not.
Im asking because Im not sure what is the best input to use for 
sclimbic anymore
The --percentile 99.9 tells it to sort all the voxels by intensity. One 
of those voxels will rank the 99.9% in intensity. All voxels that are 
brighter than this intensity are then set to this intensity 
("clipping"). This represents more closely how ScLimbic was trained. I 
will make --percentile 99.9 the default on the next release.


I decided to look at differences(correlation) of volume (.stats) 
between sclimbic or sclimbic with --percentile 99.9 ran on T1s or on 
recon all results (I wanted to make confirm the results using recon 
all subj vs t1s with the percentile flag are similar given that recon 
all does correct for bias field).  below are the correlation and 
means. this was on subsample (n=180) and I only looked at one ROI.



left BF right BF
sclimbic x sclimbic99   0.480.62
sclimbic x recon99  0.300.55
sclimbic x recon0.300.55
recon99 x recon 0.990.99
recon99 x sclimbic990.910.95
recon x sclimbic99  0.920.95


avg left BF avg BF mean
sclimbic198.77  253.96
sclimbic99  297.99  328.93
recon   312.12  340.44
recon99 315.80  343.92


(recon = sclimbic ran on recon all outputs; recon99 = sclimbic 
--percentile 99 ran on recon outputs; sclimbic=ran sclimbic on t1s; 
sclimbic99=with flag ran on t1s)


*3.so the most important question is what would you judge to provide 
the "most accurate" result to be used in subsequent group analysis. 
recon99, recon, sclimbic, or sclimbic99.

*
*This confirms my suspicions above (ie, the training). The "recon" 
method will most closely track the training (and the results from the 
paper).*


Thank you very much!
Miriam

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miriam Taza 


*Sent:* Wednesday, August 10, 2022 1:26 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain


External Email - Use Caution

but this(bright at back and nose) also seems to be the case with 
participants that sclimbic did work on..



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


*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
There was something a little strange about the cases that were failing 
-- there were very bright values at the back of the head and around 
the nose. This probably messes up the normalization in the unet. I ran 
it with --percentile 99.9 (this eliminates the extreme voxels) and the 
results looked ok after that.



On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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

*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc 
is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

__

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-11 Thread Miriam Taza

External Email - Use Caution

Hi again,

I have a few questions regarding this.

indeed it does appear that there is a bias field in all of these scans, but 
this is not specific to those that fail sclimbic.

  1.  why do you think it is consistently only the left side that fails? My 
question here is if whether it is mainly the left due to the way sclimbic does 
its magic or if this might be due to the actual data (i,e smaller left volumes 
might have an impact).

2. I would really appreciate if someone could explain what --percentile 99.9 is 
doing a bit more as my results differ a lot depending if this flag is used or 
not.
Im asking because Im not sure what is the best input to use for sclimbic 
anymore

I decided to look at differences(correlation) of volume (.stats) between 
sclimbic or sclimbic with --percentile 99.9 ran on T1s or on recon all results 
(I wanted to make confirm the results using recon all subj vs t1s with the 
percentile flag are similar given that recon all does correct for bias field).  
below are the correlation and means. this was on subsample (n=180) and I only 
looked at one ROI.


left BF right BF
sclimbic x sclimbic99   0.480.62
sclimbic x recon99  0.300.55
sclimbic x recon0.300.55
recon99 x recon 0.990.99
recon99 x sclimbic990.910.95
recon x sclimbic99  0.920.95

avg left BF avg BF mean
sclimbic198.77  253.96
sclimbic99  297.99  328.93
recon   312.12  340.44
recon99 315.80  343.92

(recon = sclimbic ran on recon all outputs; recon99 = sclimbic --percentile 99 
ran on recon outputs; sclimbic=ran sclimbic on t1s; sclimbic99=with flag ran on 
t1s)

3.so the most important question is what would you judge to provide the "most 
accurate" result to be used in subsequent group analysis. recon99, recon, 
sclimbic, or sclimbic99.

Thank you very much!
Miriam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miriam Taza 

Sent: Wednesday, August 10, 2022 1:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain


External Email - Use Caution

but this(bright at back and nose) also seems to be the case with participants 
that sclimbic did work on..


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

Sent: Tuesday, August 9, 2022 10:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

There was something a little strange about the cases that were failing -- there 
were very bright values at the back of the head and around the nose. This 
probably messes up the normalization in the unet. I ran it with --percentile 
99.9 (this eliminates the extreme voxels) and the results looked ok after that.


On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam



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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-11 Thread Douglas N. Greve

yea, this is what can happen with these deep learning algorithms -- they 
can be quite finicky. It might be that the cases that did work weren't 
as bright or did not have as many bright voxels


On 8/10/2022 1:26 PM, Miriam Taza wrote:


External Email - Use Caution

but this(bright at back and nose) also seems to be the case with 
participants that sclimbic did work on..



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


*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
There was something a little strange about the cases that were failing 
-- there were very bright values at the back of the head and around 
the nose. This probably messes up the normalization in the unet. I ran 
it with --percentile 99.9 (this eliminates the extreme voxels) and the 
results looked ok after that.



On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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

*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc 
is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-11 Thread Douglas N. Greve


Use the same command for every case

On 8/10/2022 1:15 PM, Miriam Taza wrote:


External Email - Use Caution

oh interesting, do you recommend rerunning all with -percentile 99.9? 
Would it make much difference to the results? or would it be ok to 
just run those with missing left?



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


*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
There was something a little strange about the cases that were failing 
-- there were very bright values at the back of the head and around 
the nose. This probably messes up the normalization in the unet. I ran 
it with --percentile 99.9 (this eliminates the extreme voxels) and the 
results looked ok after that.



On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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

*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc 
is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-10 Thread Miriam Taza

External Email - Use Caution

but this(bright at back and nose) also seems to be the case with participants 
that sclimbic did work on..


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

Sent: Tuesday, August 9, 2022 10:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

There was something a little strange about the cases that were failing -- there 
were very bright values at the back of the head and around the nose. This 
probably messes up the normalization in the unet. I ran it with --percentile 
99.9 (this eliminates the extreme voxels) and the results looked ok after that.


On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam



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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-10 Thread Miriam Taza

External Email - Use Caution

oh interesting, do you recommend rerunning all with -percentile 99.9? Would it 
make much difference to the results? or would it be ok to just run those with 
missing left?


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

Sent: Tuesday, August 9, 2022 10:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

There was something a little strange about the cases that were failing -- there 
were very bright values at the back of the head and around the nose. This 
probably messes up the normalization in the unet. I ran it with --percentile 
99.9 (this eliminates the extreme voxels) and the results looked ok after that.


On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.
They’re T1w scans 1x1x1mm3

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam



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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 Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-08-09 Thread Douglas N. Greve

There was something a little strange about the cases that were failing 
-- there were very bright values at the back of the head and around the 
nose. This probably messes up the normalization in the unet. I ran it 
with --percentile 99.9 (this eliminates the extreme voxels) and the 
results looked ok after that.



On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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


*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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



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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-07-29 Thread Douglas N. Greve


Can you send us a sample case?

On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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


*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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



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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-07-28 Thread Miriam Taza

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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

Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam

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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-07-28 Thread Douglas N. Greve

Have you looked at the input volume to see if there is anything strange 
about them? What kind of scans are you passing to it? What is the 
resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending 
up smaller than they should relative to right.


Thanks,
Miriam

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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

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