Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Fischl, Bruce]

Hi Carl

Did you try outputting files with names that won't be overwritten by recon-all 
for the sphere.reg and annot files and see if they are correct?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trolle, Carl
Sent: Sunday, August 28, 2022 4:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

Hi!

Thank you, yes, using the Freesurfer dev-version available through the Martinos 
cluster produced the desired result with the Destrieux-atlas. I've been using 
the 711-version throughout, I hope that I specified the version in my first 
email.

Is it possible to use these commands (mris_register and mris_ca_label) as 
expert option files during recon-all to correct the incorrect parcellation of 
the annot.aparc-file? If so, would that also require a later Freesurfer vesion 
than what we've been using?

Kind regards,

Carl
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Re: [Freesurfer] Freeview quitted unexpectedly

[fsbuild]

External Email - Use Caution

Hello Danesh,
Try putting your license.txt file into your home directory and setting the 
environment variable FS_LICENSE to point to it.
$ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should 
see your email address used to register for the license plus other license code 
…
Then try source’ing the Freesurfer script to setup the environment,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-darwin-macOS-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.3.2
FSFAST_HOME  /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR
/Applications/freesurfer/7.3.2/mni

Then try running freeview with no arguments and it should bring up an empty 
window,$ which freeview/Applications/freesurfer/7.3.2/bin/freeview$ freeview
- R.
On Aug 23, 2022, at 10:36, Danesh kajbaf daneshkaj...@gmail.com 
wrote:External Email - Use 
CautionDear support team,After 
installing Freeview, I tried to load a volume, while checking how it works with 
samples, from the subject folder in the Freesurfer folder. Unfortunately after 
choosing the file, Freeview crashed out and popped up an error message 
“Freeview quitted unexpectedly!”. I tried with other files and the same 
happened again, while all these files could be loaded by FSLeyes, so the 
problem was not with data. I run Apple Diagnostics to find if the problem was 
with the hardware or OS and there was no issue.Attached is the text file of the 
error as I copied and pasted it so it might help to tackle the problem.Freeview 
2.0 is installed ,via the Freesurfer 7.3.2 package installer, on macOS Catalina 
10.15.7, and my MacBook Pro’s part number is A1706.Regards,DaneshError 
txt.rtf___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Trolle, Carl]

Hi!

Thank you, yes, using the Freesurfer dev-version available through the Martinos 
cluster produced the desired result with the Destrieux-atlas. I’ve been using 
the 711-version throughout, I hope that I specified the version in my first 
email.

Is it possible to use these commands (mris_register and mris_ca_label) as 
expert option files during recon-all to correct the incorrect parcellation of 
the annot.aparc-file? If so, would that also require a later Freesurfer vesion 
than what we’ve been using?

Kind regards,

Carl
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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

[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 
 
 
 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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Re: [Freesurfer] FSFAST first level covariates

[Douglas N. Greve]

I was under the impression that Self and Valence were ratings from the 
same event (in that mail archive, they were different events and so 
needed different offsets). If Self and Valence are from the same event, 
then you would have something like

1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to 
demean before computing the product


On 8/14/2022 4:58 PM, Angela Fang wrote:


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The two coding schemes are different because the second one does 
include the self*valence variable you’re talking about, whereas the 
first one doesn’t. I only included the 2^nd offset because you 
suggested to someone else to include it (see *MailScanner has detected 
a possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html 
). 
If we don’t need it, would it just be 2 conditions, as follows?


 1. SelfOffset
 2. Self*ValenceSlope

But then I’m not clear how to get the main effect of valence (brain 
regions that scale with increasing emotion valence, while holding 
self-relevance constant)?


*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Sunday, August 14, 2022 at 1:37 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different? 
You can only have one offset. The Self vs Valence -a 2 -a 4 is not 
testing for an interaction. If you want an interaction you have to 
create a new variable which is SelfRating*ValenceRating.


On 8/10/2022 2:38 PM, Angela Fang wrote:

*External Email - Use Caution *

Hello,

Just re-sending my question below. If I have a variable with 2
levels (yes/no) and another variable that is continuous, based on
this post (*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html

),
it sounds like I should code as follows:

 1. SelfOffset
 2. Self-ValenceSlope (would the weight in the 4^th column reflect
the value of self multiplied by the value of valence for this
participant?)
 3. NonSelfOffset
 4. NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable
to test the interaction (as I describe below), that would also be
helpful to know.

Thanks!

Angela

*From: *
 on behalf of
Angela Fang  
*Reply-To: *Freesurfer support list


*Date: *Monday, August 1, 2022 at 4:35 PM
*To: *Freesurfer support list 

*Subject: *Re: [Freesurfer] FSFAST first level covariates

*External Email - Use Caution *

Hi Doug,

Nevermind to my first question! I read this post (*MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32235.html

)
and realized that we always include a subject-specific par file in
each run for first-level analyses.

However, I’m still confused about how to modify my paradigm file.
I also need to model the trials of non-interest, so would it be as
follows?

0 1  2.5  1.0  SelfOffset

0 2  2.5  

Re: [Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG

[Douglas N. Greve]

We did fix this at some point. Can you try running the 7.3 version to 
see if you get the same results? Often multiple threads will yield 
different results unless specifically programmed otherwise.


On 8/27/2022 4:41 AM, Giulio Siracusano wrote:


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Hi Donatas,

I've read your full paper and it is very interesting. During my 
investigation on the use of SAMSEG and ASEG for AD/MCI patients, I've 
found some unexpected behaviors.
I'm using the 7.2 version of Freesurfer and I've realized that I get 
different results using the same data but when I run the SAMSEG 
multiple times (on the same patient). This doesn't happen with ASEG.



Differently from using ASEG, SAMSEG provides also the chance to 
execute the code using multiple threads.


In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 
using the MP-RAGE series having ID I18211 (the link below provides the 
NIFTI version of the series which has been used for the processing). 
This patient is part of ADNI dataset.


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://drive.google.com/drive/folders/15oghna17Qz-OSuo9E3-rldOt935AEEuO?usp=sharing 



The first execution of SAMSEG was with default settings (1 thread) and 
results are attached, the second was using --threads 6.


These results from the SAME series are similar but they are NOT the same.

Do you have an explanation for that?

Regards


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Re: [Freesurfer] Problem with longitudinal processing (MS lesions/samseg)

[Douglas N. Greve]

If you have run recon-all on the case and samseg on the conformed image 
(eg, orig.mgz or nu.mgz), then you can run mri_surf2volseg to insert the 
cortical parcellations into the volumetic seg (look in the recon-all.log 
to see the commandline used to create the aparc+aseg.mgz)



On 8/26/2022 7:53 AM, Wittayer, Matthias wrote:


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Dear all,

thanks for the advice to use Samseg. That improved things a lot. Is 
there a way to assess more parcels than there are included in Samseg 
by default (i.e. something like aseg/astats- parcels)? I want to apply 
multivariate lonitudinal atrophy models on the data and need to 
separate i.e. frontal from parietal cortex.


Best Regards Matthias

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *Im Auftrag von *Douglas N. Greve

*Gesendet:* Freitag, 24. Juni 2022 16:22
*An:* freesurfer@nmr.mgh.harvard.edu; Cerri, Stefano 

*Betreff:* Re: [Freesurfer] Problem with longitudinal processing (MS 
lesions/samseg)


On 6/20/2022 3:03 AM, Wittayer, Matthias wrote:

*External Email - Use Caution *

Hi, thanks for your answer.
Yes I did the longitudinal runs using the base as described in the
manual. So the pipeline is:
1.) Cross sectional Recon all
2.) recon-all -base Template.nii -tp timepoint1.nii -tp
timepoint2.nii -tp timepoint3.nii -all
3.) recon all -Long timepoint1.nii Template.nii -all
Then I read volumes of the segments from asegstats from the
folders of the longitudinal runs with a R script and subtract
values of two consecutive timepoints from one another.
Miraculously some grey matter areas seem to grow in MS patients
(Not only a few voxels but up to 46%, upon visual inspection I
cannot really tell the difference as these still are just some
voxels, but in the raw data areas are pretty much the same size).
Either my boss is heading for a highly remunerated price here or I
just did something wrong with the analysis. He hopes for the
former… I am guessing the latter. The problem is not
systematically distributed as there is not for example one
timepoint that is corrupted in several areas and the others are
fine and there is not one particular area that has a problem. So
garbage in garbage out is maybe not the main problem.
The only things that came to my mind (and did not improve the
problem) were:

1.Bias field correction (I used ANTS N4), though we only have 3T-
data.

2.Lesion filling with a binary lesion mask using FSL

Do I take the right tables (asegstats from the longitudinal runs
folders) to calculate my differences?

Yes, that is right

My understanding of the longitudinal pipeline was that all
timeponits available (and not only the timeponit I do the
longitudinal run with and the next one) are used to form a
template that is warped to atlas space to measure volumes by
combinig transformation matrices of the warping of the raw
timepoint- image of the longitudinal run to the common template
and the transformation matrix of the warping of the template to
atlas space. Is that roughly the way it works?

I did not entirely follow all of that, but it sounds right. How do the 
volumes look in the cross analysis? Do you see the same trend of 
increase? When you look at the segmentations, are you saying that only 
a few voxels change even though the volume is changing by 46%? One 
thing you can try is samseg longitudinal analysis with lesion 
segmentation. It was developed  using MS lesions in mind, so it would 
be good to check on a few cases at least. I'm cc'ing Stefano who 
developed the software.



Thanks a lot!

Matthias



*Von:* freesurfer-boun...@nmr.mgh.harvard.edu

 im Auftrag von
Douglas N. Greve 

*Gesendet:* Sonntag, 19. Juni 2022 16:58:18
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Problem with longitudinal processing

When you say they are growing rather than shrinking, do you mean
in the longitudnial recon-all run? The reason I ask is that you
only mention the base and cross. When you do the longitudinal
analysis, you need to do cross, then base, then long.

On 6/15/2022 11:43 AM, Wittayer, Matthias wrote:

*External Email - Use Caution *

Dear community,

I tried to process MS- patient’s MRIs (mostly same scanner,
same settings) Longitudinally over a long period of time. I
first processed all timeponits crosssectionally and then
initialised  the base image by recon- all – base TP1 TP2 TP3
etc. Now I am trying to run label based morphometry and it
seems some areas are growing rather than shrinking. Which is
highly unlikely. I tried to exclude timepoint of a 

Re: [Freesurfer] T1 gadolinium

[Douglas N. Greve]

Not sure what you are asking or saying. Is Synthseg not useful for gad 
images or is it useful?

On 8/25/2022 10:54 AM, Gonzalo Rojas Costa wrote:
>  External Email - Use Caution
>
> Hi:
>
>SynthSeg is useful for T1-GD volumetric images? Another algorithm, 
> software?
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> https://secure-web.cisco.com/1I2XJrWdFnZxY-dYDbiZg0PV2H4bghSVXCQk63X1VSya6anSyQJv9AE2DmTqKCS_pGJ1rUzn4EKDBsMxGgxi36aU2ol9AG249ANjc-p0gshefU7IDmOWAf0BEmRpO3LG0aGtmgl5UgPE72CDm-9wFufEswwNPNCXfh1uQ236aI6nHXouVHALw32Hp3uTEHQ3epmsT3wIvNKKG2sgP0WAzYK8k7rU41-z-2aNAuANjVkUQgYO9_rOpkYYw7k6OVQtZU42sciDAzDpsVW9iIDKo2p6GecQdDYuiXNsmyUDwNTId99I2LKr6hAC6K_42OkOKcoLbSmFp1-N9gRJeKkMuVw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ
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Re: [Freesurfer] Group Analysis - glmfit results

[Douglas N. Greve]

Since this is longitudinal, I'm assuming that your contrast is actually 
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the 
the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might 
both be less than 0, but if INT is less negative than CON, then C will 
be positive and everything is working as it should (ie, there is not a 
problem or discrepancy here). What is the (complete) test that you are 
trying to accomplish?




On 8/23/2022 3:10 PM, rstei...@student.ubc.ca wrote:


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Hello Freesurfer Team,

I recently ran analysis to compare change in cortical thickness 
between an Intervention and Control group longitudinally. The contrast 
is set up as INT-CON, and therefore I would interpret a positive 
change as the intervention having a greater increase in cortical 
thickness or less atrophy than the control group.


The cluster that survived the Monte-Carlo simulation showed a positive 
difference in the LH superior parietal region when running both an 
‘abs’ and ‘pos’ simulation (these showed the same cluster.summary 
outputs). There was not a significant cluster when running the ‘neg’ 
simulation. When I compared the mean change in thickness between 
groups (cache.th13.abs.y.ocn.dat file), it showed that the control 
group experienced less atrophy than the intervention despite having a 
positive cluster output.


One possible solution I considered is accounting for baseline 
differences between groups when looking at mean change. Does glmfit 
control for baseline cortical thickness in the cluster analysis that 
is not accounted for in the mean change values from the 
cache.th13.abs.y.ocn.dat file? Is there another possible explanation 
for this discrepancy?


Thank you in advance,

Ryan S


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus 
| Musqueam Traditional Territory



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Re: [Freesurfer] Inflating norm.mgz

[Douglas N. Greve]

I'm not sure what you mean by "inflate" here. Do you just mean to run 
recon-all? Usually, you would run recon-all, then run segmentHA, then 
register the fMRI to the anatomical (bbregister), then map the segs to 
the fMRI space (mri_label2vol), then run something like mri_segstats 
--seg segs-in-fmri.mgz --ctab ctab-for-HA --excludeid 0 --avgwf 
ha-avgwf.dat --i fMRI.nii.gz

the ha-avgwf.dat will have a column for each seg in the ctab (excluding 0)

On 8/21/2022 9:57 PM, Elizabeth Haris wrote:


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Hi developers!

I am running connectivity analyses for amygdala subregions using 
images from a 7T scanner. I am wanting to transform the amygdala 
segmentations into fMRI space (1.6 iso voxel) for individual analyses 
and am looking for the best way to do this. Would it make sense to:


 1. Inflate the norm.mgz brain, then run the segmentHA_T1.sh script,
and /then/ extract the individual segments.
 2. Run the segmentHA_T1.sh script as usual, but inflate the rawavg
brain. Then, warp the full segmentation to fit the rawavg space
(using mri_convert -input  -at -rt
nearest -reference  -output
), and /then/ extract the individual
segments.

Does it matter which way I do it? Is there another way to do it that 
would be better?


Many thanks,

Elizabeth


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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Douglas N. Greve]

which version of FS are you using? There was a bug in pre 7.3.2 versions.

On 8/20/2022 11:05 AM, Fischl, Bruce wrote:


Hi Carl

Can you upload your subject including the central sulcus labels you drew?

Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Trolle, Carl

*Sent:* Friday, August 12, 2022 12:12 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution


Ok. I'm trying to attach a copy of the output I get in the 
terminal-window.


The commands I've been running for the mris_register and mris_ca_label 
are "mris_register -L subject/label/?h.central_sulcus.label 
FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central 
subject/surf/?h.sphere 
FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
subject/surf/?h.sphere.reg" and "mris_ca_label subject ?h 
subject/surf/?h.sphere.reg 
$FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs 
subject/label/?h.aparc.a2009s.annot".


I hope I'm sending what you asked for, otherwise I'll be happy to 
correct this.


Kind regards,

Carl


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Re: [Freesurfer] primary diffusion direction & surface normal vector

[Douglas N. Greve]

you can also
Convert a surface file to ascii (vertices are surface normals):
  mris_convert -n lh.white lh.white.normals.asc


On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeng, Qi 


*Sent:* Saturday, August 20, 2022 8:33 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] primary diffusion direction & surface 
normal vector


External Email - Use Caution

Hi Anastasia,

Thanks for your prompt reply. So can the normal vector of a surface be 
found in the outputs of recon-all?


Best,
Qi

On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia 
 wrote:


The principal eigenvector of the tensor, which is the primary
direction of diffusion, is V1. The magnitude of that vector is L1,
i.e., AD.

The normal vector of a surface is a vector perpendicular to the
tangent plane to the surface at a certain point. It's a
characteristic of a surface, rather than a characteristic of
diffusion, so you won't find it among the outputs of the diffusion
tensor fit.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Zeng, Qi

*Sent:* Friday, August 19, 2022 1:55 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] primary diffusion direction & surface
normal vector

External Email - Use Caution

Hi Freesurfer experts,

After DTI tensor fitting, usually we obtain primary, secondary,
and tertiary eigenvectors (V1, V2, V3) and eigenvalues (L1, L2,
L3). So what do we use to describe the primary diffusion
direction, FA or AD(=L1)? I read the term "surface normal vector"
from a paper and the formula r=[Vn * e1|. V presents the surface
normal vector, which can be computed using the cross-product
between edges. Where can I find this information?
The paper named: "Surface-based analysis of diffusion orientation
for identifying architectonic domains in the in vivo human cortex"
Thank you so much!


Best,
Qi

-- 


Ph.D. candidate
Icahn School of Medicine at Mount Sinai

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Ph.D. candidate
Icahn School of Medicine at Mount Sinai


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Re: [Freesurfer] Gyrification Index

[Douglas N. Greve]

The "Mean" column will be the mean lGI in the region

On 8/17/2022 4:42 AM, Steger Celine wrote:


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Dear FreeSurfer experts,

I try to explore the Gyrification Index of both hemispheres in a 
population. For this I computed the LGI using the Freesurfer pipeline 
and used the command suggested in previous mails:


mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex--i

$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi –excluded 0 --sum 
lh.aparc.pial_lgi.stats


Based on:(*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67629.html 
)


With this I get one line of results for this hemisphere in this 
subject in the file lh.aparc.pial_lgi.stats


….

# NRows 1

# NTableCols 10
# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev 
Min Max Range
1   1   115191   82607.4   Seg0001   3.5515   0.8629   2.1340   
5.9443  3.8103
I would like to clarify, which variable is reporting the gyrification 
index?

Thank you for your help and time.
Kind regards,
Céline Steger


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Re: [Freesurfer] mri_fill error : *** Error in `mri_fill': double free or corruption (!prev): 0x00000000014aab70 ***

[Douglas N. Greve]

Are you trying to run this from outside of recon-all? If not, can you 
send the recon-all log file? Also, have you looked at the talairach 
registration?


On 8/15/2022 7:50 AM, 丁晴 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,


I'm attempting to generate filled.mgz using the mri_fill -a 
*/ponscc.cut.log -xform  */talairach.lta 
-segementation aseg.auto_noCCseg.mgz wm.mgz filled.mgz


Error : *** Error in `mri_fill': double free or corruption (!prev): 
0x014aab70 ***


And before the error:

INFO: Using 
/home/qding/FBIP/pipeline/KM_test/2//KM002/mri/transforms/talairach.lta 
and its offset for Talairach volume ...
using segmentation 
/home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz...

reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.26345  -0.00883   0.01215  -37.76160;
 0.05445   1.62947   0.37797  -140.90414;
-0.00773  -0.25421   1.23906  -2.18153;
 0.0   0.0   0.0   1.0;
reading segmented volume 
/home/qding/FBIP/pipeline/KM_test/2//KM002/mri/aseg.auto_noCCseg.mgz

voxel to talairach voxel transform
 1.26345  -0.00883   0.01215  -37.76160;
 0.05445   1.62947   0.37797  -140.90414;
-0.00773  -0.25421   1.23906  -2.18153;
 0.0   0.0   0.0   1.0;
segmentation indicates cc at (125,  108,  153) --> (3.0, 25.0, 20.0)
Looking for area (min, max) = (350, 1400)
area[0] = 2589 (min = 350, max = 1400), aspect = 1.11 (min = 0.10, max 
= 0.75)

need search nearby
using seed (125, 108, 153), TAL = (3.0, 25.0, 20.0)

The details of bug is attached in the attachment.

The data come from a macaque.But I can use ""mri_fill" with -CV -PV to 
generate filled.mgz


I've searched the list and no similar error have been reported.

Looking forward to your reply.


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[Freesurfer] R: SAMSEG estimation error

[Cerri, Stefano]

Hi Giulio,

This is odd. I've run your scan on my computer two times using both a single 
thread and 8 threads with the default FS 7.2 and obtained the same results 
within the same number of threads.

Regarding the np.random functions, these are called only by the lesion version 
-- which, by the way, we have fixed in version 7.3 the seed to obtain 
reproducible results.

Are you sure you're running these commands on the same machine?

Stefano


Da: giulio siracusano 
Inviato: sabato 27 agosto 2022 14:15
A: Cerri, Stefano 
Cc: giulio siracusano ; 
freesurfer@nmr.mgh.harvard.edu 
Oggetto: Re: [Freesurfer] SAMSEG estimation error


External Email - Use Caution

Hi Stefano,
thanks a lot for the reply.
Unfortunately, I've realized that even when you run the same command with a 
single-thread (see attached results 1 and 3) you get slighly different results,
which are also different against the multi-thread execution (result 2).
I've checked the code in Python for samseg (in 
/usr/local/freesurfer/7.2.0/python/packages/samseg) and I can see there are 
several calls to np.random,
without setting the pseudonumber generator (such as with np.random(1234)).
This of course might have implications on the reproducibility of the results, 
although I think most of the code is in a compiled library.
You can check yourself using the file I've shared with you on google drive.
I agree with you that, based on the implementation, running SAMSEG with a 
multi-thread execution (i.e. using --threads flag) causes a non-deterministic 
behaviour and the results will not be reproducible.
Of course, we are talking about very very small variations (<0.1%) among 
results, but it is something disappointing (at least when using default 
settings which imply a single-thread execution).
Thanks for letting me know about this option when compiling the source code.

Regards

Giulio

On Sat, 27 Aug 2022 at 17:38, Cerri, Stefano 
mailto:sce...@mgh.harvard.edu>> wrote:
Hi Giulio,

Although SAMSEG is a deterministic algorithm the default version might give you 
different results when executed with a different number of threads. These are 
small differences when looking at seg.mgz (a few voxels with swapped labels), 
but they are more visible when looking at volumes computed from soft 
segmentations like the stats files.

Note that you will obtain the same exact results when running SAMSEG with the 
same number of threads.

If you want to have cross-thread reproducible results with SAMSEG you can 
download the source files of FS 7.2 and build FS with the flag 
(GEMS_CROSS_THREAD_REPRODUCIBLE ON when doing cmake). Note that this version of 
SAMSEG will run slower than the original version.

Source files can be downloaded here: 
https://github.com/freesurfer/freesurfer/tags?after=v7.3.1

and instructions on how to build FS are here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide

Hope it helps,
Stefano


Da: giulio siracusano 
mailto:siracusanogiu...@gmail.com>>
Inviato: sabato 27 agosto 2022 04:22
A: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Cerri, Stefano mailto:sce...@mgh.harvard.edu>>
Oggetto: Re: [Freesurfer] SAMSEG estimation error


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Hi Stefano,

I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2 
version of Freesurfer and I've realized that I get different results using the 
same data but when I run the SAMSEG multiple times.

Differently from using ASEG, SAMSEG provides also the chance to execute the 
code using multiple threads.

In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using the 
MP-RAGE series having ID I18211 (the link below provides the NIFTI version of 
the series which has been used for the processing).