New subject: Fw: Regression Analysis accounting for one variable

28 Nov 2019

      External Email - Use Caution
Hi,
I apologize if I did not explain my issue properly.
I'm interested in looking at age-related thickness reductions in 1 group (patients), but I'd like to also account for the effect of disease duration.
We can say that in my case disease duration is the nuisance factor.
Briefly, I have the same issue reported in here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html), but with only one group.
How would you recommend to proceed?
Many  thanks,
Pilar
________________________________
Message: 2
Date: Wed, 27 Nov 2019 16:56:20 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
        36
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: fbb77a97-61b5-fac5-e2b3-0ee327e29ce3@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
what is the difference between and independent variable and a covariate?
On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
...
     External Email - Use Caution

Yes, I did.
But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I?d like to include in the model.
How would you suggest to proceed?
Thanks,
Pilar
...
Message: 5
Date: Tue, 26 Nov 2019 21:22:34 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Regression analysis correcting for 1
      variable
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 9ac0cfa1-6e63-7d67-695e-ee607f889655@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
did you look at the one group, one variable example here?
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
On 11/25/2019 6:42 AM, Ferraro, Pilar wrote:
...
     External Email - Use Caution

Hi Freesurfer experts,
I?ve received your last response concerning the cortical thickness comparison between patients and HC correcting for disease duration and I?ve successfully completed the procedure.
Thanks again!
Now I?m contacting you cause I?m running a different analysis and I?m struggling to understand how to proceed.
In particular I would like to complete a regression analysis (only in patients, therefore only one group) looking at the effect of Variable X on cortical thickness (which I assume being higher X values corresponding to lower CT values), correcting for the effect of Variable Y (disease duration).
When I?ve looked at the Freesurfer Wiki for finding good examples I?ve thought I can use the one group, two covariates example.
However, in this case I?m not sure how the FSGD file and the matrix should be organized.
I suppose the FSGD file can simply list the Input subjects, Variable X and Variable Y.
Then the matrix should be 0 -1 0.
Am I correct?
Thanks for any help!
Pilar Ferraro
...

Message: 3
Date: Wed, 20 Nov 2019 22:40:29 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 70fa9541-d854-4530-9180-d001cf008f04@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
I responded to this a few days ago. Below is what I said
The problem is that all of your class=0 subjects have a 0 duration
meaning that you cannot compute a duration slope for this class. In this
special case, you can run a different-offset, same-slope analysis with
--fsgd dur.fsgd doss
Change your contrast matrix to 1 -1 0
On 11/19/19 5:00 AM, Ferraro, Pilar wrote:
...
????????External Email - Use Caution
Hi,
I?ve never got a response to my last email (you can find it below).
Would you be able to let me know so I can proceed with the analyses?
Many thanks,
Pilar
...
Inizio messaggio inoltrato:
*Da: *"Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu
mailto:FerraroP@pennmedicine.upenn.edu>
*Oggetto: **Fw: surface group analysis with qdec*
*Data: *14 novembre 2019 3:47:42 PM CET
*A: *"freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu"
<freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hi,
I'm trying to run a surface based group analysis comparing patients
and HC, correcting for disease duration.
I enclose here the fsgd file and the design matrix.
I've followed all the steps of the tutorial
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
no errors.
However, when I try to run the glm analysis with the following command:
mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
lh.dur.glmdir
I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
Of course there is no range for the continuous variable (disease
duration) in the control group, so I'm wondering how to overcome
this?limit and proceed correctly with the glm analysis.
Many thanks in advance for any help you will provide,
Pilar

*From:*Ferraro, Pilar
*Sent:*Monday, November 11, 2019 7:07 AM
*To:*freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:*surface group analysis with qdec
Hi!
I've previously run a comparison between patients and HC using qdec,
but now I'd like to correct the analysis for disease duration.
I've therefore generated a second qdec.table.dat file inserting the
disease duration column with the following structure:
fsid group duration
Input subj1 1 13
Input subj2 0
(For healthy controls group (group 0) I've tried both options,
leaving the duration column blank or inserting 0 as a value).
I've also left the group.level file the same of the previous analysis.
However, when i open the new qdec.table.dat file with qdec I get
problems in correctly uploading the data.
In particular, I get the following error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of continuous
variables within a class.
If you seek help with this problem, make sure to send:
?This is the command line:
?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
--fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
--glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
lh --label
/home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
/home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
Of course there is no range for the continuous variable (disease
duration) in the control group, so I'm wondering how to overcome this
and generate a?correct qdec.table.dat file.
Thanks in advance for any help!
Pilar

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Message: 4
Date: Wed, 20 Nov 2019 22:45:18 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Question about the input for longitudinal
    processing pipeline
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 8be29ed9-8627-d005-fd9b-ca3ec56f8a5b@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
I have not run images with contrast, but I think it should? work. Some
people have tried to use the mp2rage UNI scan, but it often fails
because of very bright voxels outside of the brain. If you can remove
those (eg, skull stripping), then it might work. Alternatively, if you
have a quantitative T1 that comes out of the mp2rage if you have the
license, then you can simulate an mp1rage that will then work in FS (but
it will have bias fields). If you don't have a qT1, it is not too hard
to convert the UNI to qT1. Is this at 3T or 7t?
On 11/19/19 5:35 AM, Darko Komneni? wrote:
...
????????External Email - Use Caution
Hi Douglas,
thanks for your reply. Indeed, in this particular data set they don't
all have contrast, which is unfortunate. But my question was also
general, if we assume that they all have contrast, would it be OK to
use those images as inputs in the longitudinal pipeline? And the same
question for mp2rage images, are they OK to use as well, or are they
not suitable for this pipeline?
Best,
Darko
------------------------------

Message: 11
Date: Mon, 18 Nov 2019 18:41:37 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu
<mailto:DGREVE@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Question about the input for longitudinal
? ? ? ? processing pipeline
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu
<mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"

Do all images and time points have contrast? If some do and some
don't,
then I don't think you can properly do the analysis?

On 11/15/19 10:06 AM, Darko Komneni? wrote:

...
????????External Email - Use Caution
Dear Freesurfer experts,
I wanted to run the Freesurfer's longitudinal processing pipeline
(described here
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing)
on a

...
series of MRI scans from a single patient. However, after
looking at

...
the scans, i realized that for most time points, the patient
doesn't

...
have a "simple/normal" T1 MPRAGE sequence available. Instead, they
have a T1 sequence with a contrast agent, as well as T1 mp2rage
sequences.
Is it possible/advisable to run recon-all in general or this
pipeline

...
in particular on T1 MPRAGE scans that have a contrast agent, or
that

...
are mp2rage instead of MPRAGE?
Thanks in advance!
Best,
Darko

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...
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Message: 5
Date: Wed, 20 Nov 2019 22:46:22 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 2601bc80-e87a-74b3-9227-24ca60dafd97@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
It has not changed (and is no longer supported)
On 11/19/19 6:48 AM, Steve Petersen wrote:
...
????????External Email - Use Caution
Dear Freesurfer experts,
What freesurfer version do you recommend to perform the local
gyrification index, version 6 or 6 development version?
Thanks in advance.
Best regards,

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Message: 6
Date: Wed, 20 Nov 2019 22:51:21 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 13cb3ba0-0342-6f84-2029-2d4ac0eb914e@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
This is something that is being triggered by use -3T. Is there a reason
you are using that option?
On 11/19/19 5:15 PM, Meena M. Makary wrote:
...
????????External Email - Use Caution
Hi,
I have been getting this error with one of my subjects Recon-all. I am
attaching the recon-all log file. any help would be appreciated!
Meena
--
?
*Meena M. Makary, Ph.D.*
Assistant Professor|Cairo University http://bmes.cufe.edu.eg/
Postdoctoral Fellow|Radiology, Harvard?Medical School
https://connects.catalyst.harvard.edu/Profiles/display/Person/176550
Postdoctoral Fellow| Athinoula A. Martinos Center, MGH
https://www.nmr.mgh.harvard.edu/user/4550386
Career Development and Mentoring Manager | OHBM Student and Postdoc
SIG https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449

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Message: 7
Date: Wed, 20 Nov 2019 22:54:30 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] mask for cortical thickness
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: f95d9228-9445-09c0-90d9-48f16e5a41f1@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Pass the mask you want to mri_glmfit with either --label or --mask
(depending on your format). You can convert the aparc to labels using
mri_annotation2label , then pick the label you want. In this case, you
cannot use --cache as that has been computed using whole hemi. You can
generate your own MC simulation, but the better way to do this is with
permutation. see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...
On 11/20/19 4:47 PM, Gwang-Won Kim wrote:
...
????????External Email - Use Caution
Hi there,
I would like to analyze clusterwise correction for multiple
comparisons using masks (exsample; superior frontal cortex and?middle
frontal cortex).
I know that "2spaces" means adjust p-values for two hemispheres as
follow; mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 abs
--2spaces.
If I use the masks such as the superior frontal cortex and?middle
frontal cortex,?how do I do?
Thanks,
Gwang-Won

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Message: 8
Date: Wed, 20 Nov 2019 22:58:17 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
    26
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 453c8556-e0de-cf0e-f84b-65c5273e186e@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Sorry, I don't have your fsgd file anymore. It will be computing
FirstClass-SecondClass, so red means FirstClass>SecondClass
On 11/19/19 6:05 AM, Ferraro, Pilar wrote:
...
     External Email - Use Caution

Thank you very much for your helpful reply!
I?ve kept the same fsgd file, and just edited the contrast matrix to 1 -1 0 and added the doss option to the command line, as you suggested.
I?m just a little bit confused cause now I get by default blue and red regions when I visualize the results in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC correcting for disease duration?
I just wanted to ask for a confirmation since in my fsgd file class 1 (patients) comes first and then class 0 (hc).
Many thanks,
Pilar
...

Message: 6
Date: Mon, 18 Nov 2019 18:28:58 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: surface group analysis with qdec
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: b967bd8b-5fb9-0c00-7207-3944fad5c09a@mgh.harvard.edu
Content-Type: text/plain; charset="Windows-1252"
The problem is that all of your class=0 subjects have a 0 duration
meaning that you cannot compute a duration slope for this class. In this
special case, you can run a different-offset, same-slope analysis with
--fsgd dur.fsgd doss
Change your contrast matrix to 1 -1 0
On 11/14/19 9:47 AM, Ferraro, Pilar wrote:
> ????????External Email - Use Caution
>
> Hi,
>
> I'm trying to run a surface based group analysis comparing patients
> and HC, correcting for disease duration.
> I enclose here the fsgd file and the design matrix.
> I've followed all the steps of the tutorial
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
> no errors.
> However, when I try to run the glm analysis with the following command:
>
> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
> lh.dur.glmdir
>
> I get the error:
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> --------------------------------
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
>
> Of course there is no range for the continuous variable (disease
> duration) in the control group, so I'm wondering how to overcome
> this?limit and proceed correctly with the glm analysis.
>
> Many thanks in advance for any help you will provide,
>
> Pilar
>
>
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Ferraro, Pilar
> *Sent:* Monday, November 11, 2019 7:07 AM
> *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
> *Subject:* surface group analysis with qdec
> Hi!
>
> I've previously run a comparison between patients and HC using qdec,
> but now I'd like to correct the analysis for disease duration.
> I've therefore generated a second qdec.table.dat file inserting the
> disease duration column with the following structure:
> fsid group duration
> Input subj1 1 13
> Input subj2 0
>
> (For healthy controls group (group 0) I've tried both options, leaving
> the duration column blank or inserting 0 as a value).
> I've also left the group.level file the same of the previous analysis.
> However, when i open the new qdec.table.dat file with qdec I get
> problems in correctly uploading the data.
> In particular, I get the following error:
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of continuous
> variables within a class.
> If you seek help with this problem, make sure to send:
> ?This is the command line:
> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
> lh --label
> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>
> Of course there is no range for the continuous variable (disease
> duration) in the control group, so I'm wondering how to overcome this
> and generate a?correct qdec.table.dat file.
>
> Thanks in advance for any help!
>
> Pilar
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Message: 7
Date: Mon, 18 Nov 2019 18:30:46 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] 4D multi-frame parcellation
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: ff691f12-1e79-1b2d-463b-3ae47ace83c2@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
I don't understand what you are trying to do. I'm very confused by your
mentioning of bert. What does bert have to do with any of your data?
On 11/14/19 10:47 AM, An wrote:
> ????????External Email - Use Caution
>
> Oops sorry for the mistakenly?reply. I will pay more attention in the
> future.
>
> Bert is the folder with the anatomical data. I tried the following
> steps with the 4D volume but failed. Then I checked the registration
> result after bbregister and found that the volume was not registered.
> After that I tried another 4D volume to do the steps and successfully
> got the sampled intensity onto the surface.
>
> The difference between the new 4D volume I used and the previous one
> is that there are two transformation matrices between them. The 4D
> dataset that I previously used but failed is the volume already
> registered to its anatomical volume(by using others tools). The new 4D
> volume that I tried and succeed is the volume not registered.
>
> I have no idea why the 4D volume after the transformation would cause
> a failed result. Could you please let me know that?
>
> Many thanks.
>
> Best,
> An
>
> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
> mailto:DGREVE@mgh.harvard.edu> ?2019?11?13??? ??12:20???
>
>     If you have an anatomical MR that you have run through recon-all,
>     then
>     just use that one instead of bert in your steps below
>     ps. Please remember to post to the FS list and not to us personally
>
>     On 11/12/19 8:41 PM, an wrote:
>> ????????External Email - Use Caution
>>
>> Many thanks.
>>
>> I got the 4D fMRI dataset from others and it is not raw data. In
>     order
>> to run mri_vol2surf, I need to calculate the register.dat for the
>> required flag --srcreg so I tried in this way.
>>
>> FYI, the 4D fMRI dataset should have been registered with its
>> anatomical MR volume by using other tools.
>>
>> For now I only ran the recon-all on its anatomical MR volume
>     without
>> running the functional stream as I don't have the raw data.
>>
>> Should I also run the raw fMRI data from scratch by using
>     functional
>> stream? Or if I can run mri_vol2surf independently, which command
>> should I use to get a register.dat file?
>> In addition, the intensity of the 4D fMRI dataset I have is between
>> [-1, 1] and not integers, would this cause any problem?
>>
>> Best,
>> An
>>
>>
>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>> Don't do the 1st step.
>>> Why are you registering it to bert? I'm pretty sure bert did not
>>> participate in your fmri study
>>> When you run mri_vol2surf, it will probably work better with
>>> --projfrac 0.5
>>>
>>> On 11/11/2019 1:32 PM, An wrote:
>>>> ????????External Email - Use Caution
>>>>
>>>> Hi Prof. Greve,
>>>>
>>>> Thanks for your reply and sorry for the confusion.
>>>>
>>>> I have a 4D fMRI dataset with 10 time frames, where the
>     intensity of
>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>> intensities of the volumes on its corresponding surface in
>     order to
>>>> get the functional values on each vertex in each frame. I have
>>>> already run its corresponding anatomical image in freesurfer.
>>>>
>>>> To achieve it, I tried the following steps:
>>>> 1. conform the fmri series by using mri_convert
>>>> 2. register the fmri series with the anatomy image by using
>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>     register.dat
>>>> 3. assign values from volumes to each vertex by using
>     mri_vol2surf:
>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>> register.dat --hemi lh
>>>> ? ? I also tried the -regheader in mri_vol2surf: mri_vol2surf
>     --src
>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>
>>>>
>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>     freeview. But
>>>> after step2, the registered volume looks wrong. I am wondering
>     could
>>>> I use bbregister to register multi-frame fMRI series to a single
>>>> volume?
>>>> I also tried to use --regheader to replace the --srcreg file in
>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>     the
>>>> output is still wrong.
>>>>
>>>> Many thanks.
>>>>
>>>> Best,
>>>> An
>>>>
>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>     mailto:DGREVE@mgh.harvard.edu
>>>> mailto:DGREVE@mgh.harvard.edu
     mailto:DGREVE@mgh.harvard.edu>> ?2019?11?11??? ??12:16???
>>>> ? ? ?When you say it is 4D, what do you mean? That each label
>     has its
>>>> ? ? ?own frame?
>>>>
>>>> ? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>> ? ? ?>
>>>> ? ? ?> ????????External Email - Use Caution
>>>> ? ? ?>
>>>> ? ? ?> Hi there,
>>>> ? ? ?>
>>>> ? ? ?> I am working with creating a surface parcellation from a
>>>> ? ? ?volumetric
>>>> ? ? ?> parcellation and have some questions as follows:
>>>> ? ? ?>
>>>> ? ? ?> 1. If the volumetric parcellation is a labeled 4D
>     multi-frame
>>>> ? ? ?dataset,
>>>> ? ? ?> could I still use the mris_sample_parc? Or could
>     mri_vol2surf
>>>> ? ? ?get the
>>>> ? ? ?> sampled labels for every vertex?
>>>> ? ? ?>
>>>> ? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>> ? ? ?results,
>>>> ? ? ?> which GUI should I use to visualize it? I tried freeview
>     for 4D
>>>> ? ? ?> multi-frame dataset but it looks weird.
>>>> ? ? ?>
>>>> ? ? ?> 3. Is there any command to separate?multi-frame volume to
>>>> ? ? ?single frame
>>>> ? ? ?> volumes?
>>>> ? ? ?>
>>>> ? ? ?> Many thanks!
>>>> ? ? ?>
>>>> ? ? ?>
>>>> ? ? ?> Best,
>>>> ? ? ?> An
>>>> ? ? ?>
>>>> ? ? ?> _______________________________________________
>>>> ? ? ?> Freesurfer mailing list
>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>     mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> ? ? ?mailto:Freesurfer@nmr.mgh.harvard.edu
     mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ?_______________________________________________
>>>> ? ? ?Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>     mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> ? ? ?mailto:Freesurfer@nmr.mgh.harvard.edu
     mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>     mailto:Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>     mailto: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
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>     but does not contain patient information, please contact the
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Message: 8
Date: Mon, 18 Nov 2019 18:31:35 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Multiple comparisons
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: 745185b7-5ebb-43bf-6d2d-b7328622fe5f@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
My preferred method is to use permutation
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...
On 11/14/19 12:29 PM, Juan Rivas wrote:
> ????????External Email - Use Caution
>
> I would like to know how the correction is made for multiple
> comparisons in the statistical analysis? We are using QDEC, with False
> Discovery Rate or Montecarlo Null-Z. Is there a better way to do that?
> Best,
> JC.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Message: 9
Date: Mon, 18 Nov 2019 18:38:43 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Questions for PetSurfer
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: f98e29f6-3532-91ed-021f-1e947468f57f@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
On 11/15/19 4:19 AM, Soo-Jong Kim wrote:
> ????????External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am a student in neuroimaging using FreeSurfer.
> I have some questions and I don't know where to send questions.
> That's why I found this mail and writing.
>
> I've studied PetSurfer for partial volume correction of PET.
> I saw the tutorial in website.
> Originally, I want to use RBV method for pvcorrected PET for SUVR
> analysis.
>
> After generating gtmseg and coregistration to make lta file, I
> followed this code and changed some.
>
> *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz *
> *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov
> --rbv --o output_pvc*
>
> After this, rbv.nii.gz file was generated. and SUVR analysis was
> performed as reference region (cerebellar cortex).? But Compared to
> original un-pvc PET, Cortex SUVR was reduced...
>
> In ideal pv-corrected PET, cortex SUVR was higher than?un-pvc PET.
>
> Is is okay if I use the output file as rbv.nii.gz ?
Yes, it does work. Is your tracer one where you expect GM > WM?
> in Thomas et al, 2011,
> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
> Frontal, Temporal, Occipital and so on. (Only gray matter to correct
> PET using RBV method)
>
> In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz)
> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
Yes
> If not, Please tell me what is the correct command of mri_gtmpvc.
> I need only partial volume corrected PET using RBV method.
>
> Sincerely,
>
> Soo-Jong Kim
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Message: 10
Date: Mon, 18 Nov 2019 18:39:32 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical thickness values on a vertex base
  level
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0@mgh.harvard.edu
Content-Type: text/plain; charset="Windows-1252"
The sig file
On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote:
> ????????External Email - Use Caution
>
> Thank you so much for your repsonse.
> Could you maybe please tell us which input file we should use?
>
> Best wishes,
> AIcha
> ------------------------------------------------------------------------
> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
> freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas
> N.,Ph.D. DGREVE@mgh.harvard.edu
> *Verzonden:* donderdag 31 oktober 2019 19:16
> *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
> base level
> You can run mri_surfcluster with your fdr threshold as the --thmin
> value. This will output cluster number (ocn) map. This will assign the
> cluster number to a vertex. You can then use mri_segstats with --seg
> ocn.mgz --excludeid 0 and input being the mean thickness or area maps.
> When you use area as thhe input, make sure to --accumulate to get the
> total area. You can get an area map in the same way that you got the
> thickness map, ie, mris_preproc, etc
>
> On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>> ????????External Email - Use Caution
>>
>> Dear Greve,
>>
>> Thank you for your quick respons.
>>
>> Yes, I believe that is what I mean. Let me illustrate with some
>> (fictive) data;
>> We were able to prove these data for the entire hemisphere as can be
>> seen below.
>>
>>
>>
>>
>>
>> *Group 1*
>>
>>
>>
>> *Group 2*
>>
>>
>>
>> *Difference*
>>
>>
>>
>> */Sig./*
>>
>> Thickness
>>
>> (in mm)
>>
>>
>>
>> Left
>>
>>
>>
>> 1.48
>>
>>
>>
>> 1.46
>>
>>
>>
>> .004
>>
>>
>>
>> .19
>>
>> Right
>>
>>
>>
>> 1.46
>>
>>
>>
>> 1.46
>>
>>
>>
>> .003
>>
>>
>>
>> .03
>>
>>
>>
>>
>>
>>
>> However, we would like to provide similar data in our vertex-base
>> analyses:
>>
>> *Significantly different clusters between group 1 and group 2*
>>
>>
>>
>> *Cortical thickness group 1*
>>
>>
>>
>> *Cortical thickness group 2*
>>
>>
>>
>> *Difference in mm2*
>>
>>
>>
>> */Sig./*
>>
>> Left Cuneus
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> 0.013
>>
>> Left Fusiform gyrus
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> 0.021
>>
>> Right Paracentral lobule
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> 0.001
>>
>> Right parahippocampal gyrus
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> ?
>>
>>
>>
>> 0.002
>>
>>
>> Does this clarify my question?
>>
>> Best wishes,
>> Aicha
>>
>>
>>
>> ------------------------------------------------------------------------
>> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
>> freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas
>> N.,Ph.D. DGREVE@mgh.harvard.edu
>> *Verzonden:* donderdag 31 oktober 2019 16:25
>> *Aan:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
>> base level
>> I'm not sure what you mean. Do you want the mean thickness of a cluster
>> and/or its surface area?
>>
>> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>>> ????????External Email - Use Caution
>>>
>>> Dear developers,
>>>
>>> For a case-control study we are comparing the cortical thickness and
>>> cortical surface area on a vertex-base level, for which we found
>>> significant differences throughout the brain.
>>>
>>> Is it possible that, in addition to the significance values (p < .05
>>> after FDR correction) on a vertex-base level, we can include the exact
>>> thickness or surface area value (or difference) of the significant
>>> clusters on a vertex base-level between the groups. In order words, to
>>> provide some measures to highlight the size of the significant cluster
>>> or the differences in cortical thickness / cortical surface area to
>>> provide clinically useful context. For instance, a command comparable
>>> to 'voxel size' in TBSS.
>>>
>>> As this is my first time using Freesurfer any help that you could
>>> offer on this matter would be highly appreciated.
>>>
>>> Best wishes,
>>> Brigitte Dijkshoorn
>>>
>>> _______________________________________________
>>> 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
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Message: 11
Date: Mon, 18 Nov 2019 18:41:37 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Question about the input for longitudinal
  processing pipeline
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Do all images and time points have contrast? If some do and some don't,
then I don't think you can properly do the analysis?
On 11/15/19 10:06 AM, Darko Komneni? wrote:
> ????????External Email - Use Caution
>
> Dear Freesurfer experts,
> I wanted to run the Freesurfer's longitudinal processing pipeline
> (described here
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
> series of MRI scans from a single patient. However, after looking at
> the scans, i realized that for most time points, the patient doesn't
> have a "simple/normal" T1 MPRAGE sequence available. Instead, they
> have a T1 sequence with a contrast agent, as well as T1 mp2rage
> sequences.
>
> Is it possible/advisable to run recon-all in general or this pipeline
> in particular on T1 MPRAGE scans that have a contrast agent, or that
> are mp2rage instead of MPRAGE?
>
> Thanks in advance!
> Best,
> Darko
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Message: 12
Date: Mon, 18 Nov 2019 18:45:17 +0000
From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu
Subject: Re: [Freesurfer] Brain lobules pooling- request
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID: a457c4e8-913e-706e-c7ef-8925c7eaad3d@mgh.harvard.edu
Content-Type: text/plain; charset="Windows-1252"
sorry, it is not clear to me what is going wrong here. Did the
mri_annotation2label command fail? or mris_anatomical_stats command?
On 11/17/19 9:55 PM, Samson Nivins wrote:
> ????????External Email - Use Caution
>
> Hi FreeSurfer Team,
>
> ????? I am interested in individual lobular volume and thickness. So I
> have extracted based on the Q and A I created few script to run and
> extract the data.
>
> However, I got few questions regarding thickness and WM
>
> For extracting lobular GM I used
>
> mri_annotation2label --subject 1014? --hemi lh --lobesStrict
> lh.lobesStrict.annot
>
> mri_annotation2label --subject 1014? --hemi lh --annotation
> lobesStrict --outdir
> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh'
>
> for computing stats I used
>
> mris_anatomical_stats -l
> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label'
> -b 1014 lh
>
> I am not sure, whether any command is there to export the data.
>
> And, the average cortical thickness which we obtain in the terminal
> window during individual extraction, does it correspond to the lobular
> thickness or as whole
>
> For example
>
> I extracted stats for left frontal cortex:
>
> I got the following details in Terminal window
>
> Number of vertices, Total surface area, total gray matter, average
> cortical thickness ?.
>
> In this average cortical thickness ? correspond to the ROI specifc are
> as a whole?
>
> Thanks for you help.
>
> Looking forward to hearing from you
>
> Cheers
>
> Best regards,
>
> Sam
>
> *Samson Nivins? |**PhD Student*
>
> **
>
> *A*The University of Auckland, Liggins Institute
>
> Building 505, Level 2, 85 Park Road, Auckland
>
> *Ph *+(64) 21 256 5964
>
> *E*samson.nivins@gmail.com mailto:samson.nivins@gmail.com
>
> *//*
>
> cid:image001.png@01D4C1F6.9273DF90
>
>
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Message: 13
Date: Mon, 18 Nov 2019 13:48:58 -0500
From: An annaqu1024@gmail.com
Subject: Re: [Freesurfer] 4D multi-frame parcellation
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID:
  CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA@mail.gmail.com
Content-Type: text/plain; charset="utf-8"
    External Email - Use Caution

I want to map the intensities of the volumes on its corresponding surface
in order to get the functional values on each vertex in each frame. I ran
recon-all for the anatomical volume and saved all outputs(mri,labels,surf
and etc.) in the bert folder. I use it because I need to specify the
required flag -s in bbregister in order to register the functional volume
to its anatomical volume.
Many thanks.
Best,
An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu ?2019?11?18??? ??1:31???
> I don't understand what you are trying to do. I'm very confused by your
> mentioning of bert. What does bert have to do with any of your data?
>
> On 11/14/19 10:47 AM, An wrote:
>>         External Email - Use Caution
>>
>> Oops sorry for the mistakenly reply. I will pay more attention in the
>> future.
>>
>> Bert is the folder with the anatomical data. I tried the following
>> steps with the 4D volume but failed. Then I checked the registration
>> result after bbregister and found that the volume was not registered.
>> After that I tried another 4D volume to do the steps and successfully
>> got the sampled intensity onto the surface.
>>
>> The difference between the new 4D volume I used and the previous one
>> is that there are two transformation matrices between them. The 4D
>> dataset that I previously used but failed is the volume already
>> registered to its anatomical volume(by using others tools). The new 4D
>> volume that I tried and succeed is the volume not registered.
>>
>> I have no idea why the 4D volume after the transformation would cause
>> a failed result. Could you please let me know that?
>>
>> Many thanks.
>>
>> Best,
>> An
>>
>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>> mailto:DGREVE@mgh.harvard.edu> ?2019?11?13??? ??12:20???
>>
>>     If you have an anatomical MR that you have run through recon-all,
>>     then
>>     just use that one instead of bert in your steps below
>>     ps. Please remember to post to the FS list and not to us personally
>>
>>     On 11/12/19 8:41 PM, an wrote:
>>>         External Email - Use Caution
>>>
>>> Many thanks.
>>>
>>> I got the 4D fMRI dataset from others and it is not raw data. In
>>     order
>>> to run mri_vol2surf, I need to calculate the register.dat for the
>>> required flag --srcreg so I tried in this way.
>>>
>>> FYI, the 4D fMRI dataset should have been registered with its
>>> anatomical MR volume by using other tools.
>>>
>>> For now I only ran the recon-all on its anatomical MR volume
>>     without
>>> running the functional stream as I don't have the raw data.
>>>
>>> Should I also run the raw fMRI data from scratch by using
>>     functional
>>> stream? Or if I can run mri_vol2surf independently, which command
>>> should I use to get a register.dat file?
>>> In addition, the intensity of the 4D fMRI dataset I have is between
>>> [-1, 1] and not integers, would this cause any problem?
>>>
>>> Best,
>>> An
>>>
>>>
>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>> Don't do the 1st step.
>>>> Why are you registering it to bert? I'm pretty sure bert did not
>>>> participate in your fmri study
>>>> When you run mri_vol2surf, it will probably work better with
>>>> --projfrac 0.5
>>>>
>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>         External Email - Use Caution
>>>>>
>>>>> Hi Prof. Greve,
>>>>>
>>>>> Thanks for your reply and sorry for the confusion.
>>>>>
>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>     intensity of
>>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>>> intensities of the volumes on its corresponding surface in
>>     order to
>>>>> get the functional values on each vertex in each frame. I have
>>>>> already run its corresponding anatomical image in freesurfer.
>>>>>
>>>>> To achieve it, I tried the following steps:
>>>>> 1. conform the fmri series by using mri_convert
>>>>> 2. register the fmri series with the anatomy image by using
>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>     register.dat
>>>>> 3. assign values from volumes to each vertex by using
>>     mri_vol2surf:
>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>> register.dat --hemi lh
>>>>>     I also tried the -regheader in mri_vol2surf: mri_vol2surf
>>     --src
>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>
>>>>>
>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>     freeview. But
>>>>> after step2, the registered volume looks wrong. I am wondering
>>     could
>>>>> I use bbregister to register multi-frame fMRI series to a single
>>>>> volume?
>>>>> I also tried to use --regheader to replace the --srcreg file in
>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>>     the
>>>>> output is still wrong.
>>>>>
>>>>> Many thanks.
>>>>>
>>>>> Best,
>>>>> An
>>>>>
>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>     mailto:DGREVE@mgh.harvard.edu
>>>>> mailto:DGREVE@mgh.harvard.edu
>     mailto:DGREVE@mgh.harvard.edu>> ?2019?11?11??? ??12:16???
>>>>>     When you say it is 4D, what do you mean? That each label
>>     has its
>>>>>     own frame?
>>>>>
>>>>>     On 11/6/19 5:59 PM, ?? wrote:
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> I am working with creating a surface parcellation from a
>>>>>     volumetric
>>>>>> parcellation and have some questions as follows:
>>>>>>
>>>>>> 1. If the volumetric parcellation is a labeled 4D
>>     multi-frame
>>>>>     dataset,
>>>>>> could I still use the mris_sample_parc? Or could
>>     mri_vol2surf
>>>>>     get the
>>>>>> sampled labels for every vertex?
>>>>>>
>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>>>     results,
>>>>>> which GUI should I use to visualize it? I tried freeview
>>     for 4D
>>>>>> multi-frame dataset but it looks weird.
>>>>>>
>>>>>> 3. Is there any command to separate multi-frame volume to
>>>>>     single frame
>>>>>> volumes?
>>>>>>
>>>>>> Many thanks!
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>     mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>     mailto:Freesurfer@nmr.mgh.harvard.edu
>     mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> _______________________________________________
>>>>>     Freesurfer mailing list
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Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue 38

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08