Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

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Hi Dr. Greve,

Thank you very much for your solution. That solved the problem.

I genuinely appreciate your support!

Best,
Hyunwoo Jeong

2022년 3월 10일 (목) 오전 2:52, Douglas N. Greve 님이 작성:

> The problem is that your design matrix is badly scaled. The eTIV values
> are much larger than the group membership (value=1). Try subtracting the
> mean of the eTIV and dividing by the stddev to normalize it.
>
>
> On 2/25/2022 8:07 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files
> that I used to run the mri_glmfit command. I can upload the recon-all
> outputs of the individual samples as well, if needed. The files are
> uploaded in google drive, please access them via the link below.
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1OSqR9RniGPyWuFMchLKO678Wi2STTGhXTdrWB93Dvxpp0D8X0W8OLeVfExQQz7p0kQqayDn3ySQxM9CxrtY8igbR9kqzlm7l90460XSu1uKZC4NzDn_HBkQQ1NPMMyb1RuV_1vYGs_m3H7VdUayjO88cs1-DTC8eAnsE8WsPcGfMw-CevWVhDu3mlbBBooXuPA01rU6yPLXYtR32L3KgIZF3UHHOl0Os4dsciWtU0mlHS4Tuvy4KzqrpbRbB19sXGcDUgtjIfpDfZMgROJjI5_4eDgKgTQtDtcI3_7jweaVpaEt915oj4PQ0N-kaSm4D/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing
> 
>
> Thank you in advance,
> Hyunwoo Jeong.
>
>
>
> 2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 님이 작성:
>
>> Can you upload the data to me somewhere? I'd need the input volume and
>> the fsgd and any contrasts
>>
>> On 2/21/2022 10:24 PM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hi Dr. Greve,
>>
>> Thank you for your suggestion. Unfortunately, the same problem occurred
>> when I ran the command with --no-pcc. Folders and files with the same names
>> were created. and the following error message (identical to the previous
>> one) appeared.
>>
>> error: No such file or directory
>> error: MatrixMultiplyD(): m2 is null
>>  break
>> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>>
>> Do you have any other suggestions? I appreciate your help so far.
>>
>> Best,
>> Hyunwoo Jeong
>>
>> 2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:
>>
>>> Hi Dr. Greve,
>>>
>>> Thank you for your suggestion. Unfortunately, the same problem occurred
>>> when I ran the command with --no-pcc. Folders and files with the same names
>>> were created. and the following error message (identical to the previous
>>> one) appeared.
>>>
>>> error: No such file or directory
>>> error: MatrixMultiplyD(): m2 is null
>>>  break
>>> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>>>
>>> Do you have any other suggestions? I appreciate your help so far.
>>>
>>> Best,
>>> Hyunwoo Jeong
>>>
>>> 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이
>>> 작성:
>>>
 It looks like it is failing when computing the partial correlation
 coef. Try  running it with --no-pcc

 On 2/16/2022 10:53 AM, 정현우 wrote:

 External Email - Use Caution
 Hi Dr. Greve,

 Yes, it seems like the output folder and some output files were created.

 After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
 folder was created. In the glmdir folder, 'three_group_comparison.area'
 folder was created, and the following files were also created: beta.mgh,
 dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
 sar1.mgh, surface, and Xg.dat.

 In the 'three_group_comparison.area' folder, the following files were
 created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.

 Do you have any idea what could have been the problem?

 Thanks,
 Hyunwoo Jeong

 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이
 작성:

> Did it create the output folder and some output files? I noticed that
> there is a "error: No such file or directory" error 
>
> On 2/14/2022 8:46 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your reply. I attached the fsgd file, mtx file and the
> Xg.dat file below.
>
> Hyunwoo Jeong
>
> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이
> 작성:
>
>> can you send your fsgd file and the Xg.dat file?
>>
>> On 2/14/2022 1:21 AM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hello 

Re: [Freesurfer] recon-all permissions problems

[fsbuild]

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Hello Giuseppe,
Try the same command (with lowercase w) or use a+w and then enter your password,
$sudo chmod -R a+w $SUBJECTS_DIRPassword:
… then test to see if it works to create a file there, i.e., it should not 
report permission denied ...
$ touch $SUBJECTS_DIR/foo
… then see if you can remove the file …
$ rm $SUBJECTS_DIR/foo
If that works you should be OK.
- R.
On Mar 6, 2022, at 11:46, giuseppe messina gius...@gmail.com 
wrote:External Email - Use 
Cautionhi i am a neurosurgeon, 
and i am a newbie in freesurfer, nut i thin i installed it appropriately and 
the licence txt file is oki have a macbookpro16 last generation with 32 
gb of memorymy freesurfer version is 7.2.0the problem is that when i run 
recon-all ( in correct syntax) , permission issues appear; it seems that i 
donthave permissions to go ahead with the freesurfer.i also used ( as 
indicated in one of your tutorial ) the sudo chmod -R a+W $SUBJECTS_DIR 
command, but if i do so, a password is requested in the terminal.really, i 
dontknow hot to solve this problem, please help meGiuseppeThank you 
again--Giuseppe MessinaDept NeurosurgeryIstituto Nazionale Neurologico 
"Carlo Besta", 
MilanE-mailgiusmex@gmail.com___Freesurfer
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Re: [Freesurfer] Oracle VM - SSH

[fsbuild]

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Hello Zoe,
The VM is not setup out of the box with an IP address you can use to remotely 
login to from an outside machine. It uses (or piggy-backs off) the 
existing network connection from the host machine.  This enables the VM 
to boot w/o needing to negotiate for a non-local IP address and it is also for 
security. We don't know the policy for someone connecting a new (virtual 
or real physical) machine to the network the host machine is already using. 
If you can remotely VNC into your host machine and see/use the desktop, 
then you can use the VM running on the desktop as just another application.

There’s information available online about how setup a VirtualBox VM to be 
accessible from the outside, e.g., via ssh.  If you have IT support, you 
could ask them for help. But it’s not really practical for us to support 
users configuring a machine to run on their local network.
On Mar 9, 2022, at 14:44, Zoe O'Brien-Moran zobrienmo...@cubresa.com 
wrote:External Email - Use 
CautionHello FS expertsI'm 
using freesurfer with the oracle VM and I need to SSH in from my host machine, 
I see that openSSH is installed on the VM, but haven't been able to get 
in.Does anyone have experience with/ advice for this?Thanks in 
advanceZoë___Freesurfer 
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[Freesurfer] Oracle VM - SSH

[Zoe O'Brien-Moran]

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Hello FS experts

I'm using freesurfer with the oracle VM and I need to SSH in from my host 
machine, I see that openSSH is installed on the VM, but haven't been able to 
get in.

Does anyone have experience with/ advice for this?

Thanks in advance

Zoë
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[Freesurfer] Atlas of primary motor and auditory cortex

[Jingyi Wang]

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Hello Freesurfer experts,

I ran the recon-all command and got all the .label files for the
segmentations of the cortical areas. However, I have some questions about
the label for primary motor and auditory cortex.

   - I found two types of labels associated with the primary motor
   cortex: lh.L_M1.label and lh.BA4a_exvivo.label. Are they both valid, and
   the lh.BA4a_exvivo.label segmentations are finer parcellation than the
   other one?
   - What's the primary auditory cortex .label file?

Thanks in advance!

Jingyi Wang
Postdoctoral Scholar
LEAP Neuro Lab
Psychological & Brain Sciences
University of California, Santa Barbara
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Re: [Freesurfer] Cutting the Full Surface

[Francesca Strappini]

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Thank you!

On Wed, Mar 9, 2022, 19:28 Douglas N. Greve  wrote:

> In FreeView
> Click on the brain with scissors icon ("Cut"), select your points, then
> "Cut Closed Line",
>make sure the cusror is in the patch, then hit "Fill Uncut Area", then
> save as a patch
>
>
> On 3/7/2022 12:03 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Dear FreeSurfer experts,
>
> I'm trying to cut and flatten the full surface. I understand that tksurfer
> is deprecated and on my PC does not work properly. Is there an alternative
> way to perform the cuts?
>
> Thank you,
> Francesca
>
>
>
> --
> Francesca Strappini, Ph.D.
> Psychology Department
> Sapienza University of Rome
> Via dei Marsi 78, Rome 00185 Italy
> Tel.: +39 392 151 4029
> E-mail: francesca.strapp...@uniroma1.it
> 
>
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Re: [Freesurfer] Cutting the Full Surface

[Douglas N. Greve]

In FreeView
Click on the brain with scissors icon ("Cut"), select your points, then 
"Cut Closed Line",
   make sure the cusror is in the patch, then hit "Fill Uncut Area", 
then save as a patch



On 3/7/2022 12:03 PM, Francesca Strappini wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I'm trying to cut and flatten the full surface. I understand that 
tksurfer is deprecated and on my PC does not work properly. Is there 
an alternative way to perform the cuts?


Thank you,
Francesca



--
Francesca Strappini, Ph.D.
Psychology Department
Sapienza University of Rome
Via dei Marsi 78, Rome 00185 Italy
Tel.: +39 392 151 4029
E-mail: francesca.strapp...@uniroma1.it 



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Re: [Freesurfer] recon-all errors after mri_pretess

[Douglas N. Greve]

Does this fail every time like this? It looks like it just abruptly 
stopped. Does anything print out to standard error?


On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:


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Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting 
errors on our cluster (CentOS 8)


The attached recon-all.log file is attached for details. The last 
several lines of the file are below. Any comments as to why its 
failing? Jim.


pass   1 (--):   0 found -   0 modified |    TOTAL:   0

pass   1 (-+):   0 found -   0 modified |    TOTAL:   0

Total Number of Modified Voxels = 631 (out of 421942: 0.149547)

binarizing input wm segmentation...

Ambiguous edge configurations...

mri_pretess done

@#@FSTIME  2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 
96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45


@#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45

#

#@# Fill Thu Mar  3 12:52:02 CST 2022



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Re: [Freesurfer] Using T1 FLAWS in recon-all

[Douglas N. Greve]

never heard of FLAWS. My good search says that it is WM and CSF 
suppression, so it probably won't work.


On 3/4/2022 6:10 AM, Mathilde Pichon wrote:


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Hello,

I know T1 MPRAGE is the prefered format to perform a recon-all 
segmentation.

But some of my patients' data only have FLAWS images and no MPRAGE images.
So is it possible to perform a recon-all with FLAWS images ?

Regards,

Mathilde

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Re: [Freesurfer] ERROR: Flag -sveres unrecognized

[Douglas N. Greve]

What version are you trying to run? selxavg-sess has been depricated for 
years. Try selxavg3-sess


On 3/3/2022 10:59 AM, CALLACHAND Muntasir wrote:


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Hi,

I have a problem when i try to run the function selxavg-sess 
 
with the optional arguments -sveres. This message occur :


ERROR: Flag -sveres unrecognized

Do you know what i can do to fix this?

Best,
Muntasir CALLACHAND

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Re: [Freesurfer] Error: inputs cannot have multiple frames

[Douglas N. Greve]

It means that you have two frames in the 001.mgz file. Sometimes this 
happens with multiecho mprages. If this  is the case, you can convert 
your input to a single frame with

mri_concat --rms file.mgz --o file.rms.mgz
Then use file.rms.mgz as the input to recon-all

On 3/3/2022 12:04 AM, HYE JUNG YOUN wrote:


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Dear Freesurfer developers,

I realised some of my recon-alls been processed with the following error:

ERROR: input(s) cannot have multiple frames! 
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames


(I have attached the recon-all.log)

I checked the mri info and I think the problem is the dimensions which 
is 256 x 256 x 211 x 2.


I’ll attach the original commands I used with mri info in txt file in 
case it would help you to see where I went wrong.


If anyone has been through this problem or if you know what I can do 
to fix this, please let me know.


Best,

H


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Re: [Freesurfer] bbregister dependencies recon-all

[Douglas N. Greve]

You pretty much have to run it through to the end. You can try using 
mri_coreg (this is the first step of bbregister). It does not need 
anything but two images and will  run in  a few min.

On 3/3/2022 5:24 AM, Guillem París wrote:
>  External Email - Use Caution
>
> Hello,
>
> I'm trying to run a Boundary-based registration by using bbregister. In
> the documentation, it is specified that the anatomical image has to be
> previously analysed in FreeSurfer. I assume that means to run the
> "recon-all" pipeline.
>
> Now, are all the stages of "recon-all -all" needed to perform this
> registration? Since I am time-constrained, I would like to run as few
> stages as possible, so I can use bbregister.
>
> If it matters, I'm trying to register a DWI to the same subject's T1-w.
>
> Thank you!
>
> Guillem
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] GLM analysis - volume and surface area

[Douglas N. Greve]

Can you just ask the question again so I don't have to sort it out myself?

On 3/2/2022 3:30 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Sorry about that!

I'm resending with previous emails.

The first message below is the one you didn't know how to respond to 
because you didn't have the previous e-mails.


---

On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:

Thanks so much for the explanation!

There is something different in the analysis of volume and surface 
area in relation to the analysis of cortical thickness? Like some more 
command, or some other detail that must be changed (besides, of 
course, the flag that specifies the measure to be analyzed) - I'm 
already using permutation in the correction of multiple comparisons.




--

On 2/21/2022 15:20 PM, Douglas N. Greve wrote:

Yes, it is. It is confusing when you talk about area and volume 
sincethese are not point measures like thickness (ie, what is the 
volume orarea of a vertex?). The area of a vertex is computed as the 
mean of theadjacent triangles of the vertex. The volume is the mean of 
theneighboring truncated tetrahedra. When you run mris_preproc, it 
willapply a jacobian correction (like VBM). Otherwise, it operates the 
sameas if you had a thickness value at the vertex, ie, same GLM, etc. 
Makesure to use permutation for correction of multiple comparisons.


-

On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:

Hello FreeSurfer Developers,

I would like to know if it is correct to perform volume and
surfacearea analysis using freesurfer's GLM!?

In several mailing list questions I have already seen instructions
forperforming these types of analysis. But I understand that
freesurferdoes vertex-wise analysis in the 2D surface space. So,
it is not clearto me how it is possible to evaluate a 3D
measurement, as volume, witha 2D method!?

I've also read that surface area analysis via vertex-wise
analysisdoesn't make much sense. The best would be to do ROI-based
analysis.Can you explain that to me?

Thanks in advance!

Best,

Laura.


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Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

Do you have permission to /scratch? Does it exist?

On 3/2/2022 9:50 AM, Billah, Tashrif wrote:

Hi all,

We are trying to run recon-all with -localGI but running into an 
unknown permission denied error:


$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); 
exit

=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading
ERROR: loading 
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz 
as MGH

Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file 
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!



recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other 
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.


Best,
Tashrif

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Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Caitlin R Bowman]

External Email - Use Caution

Tried it, but I still get the same error.

--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee

From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 8, 2022 at 3:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace (captured):
[  0] 0x2baa65422f4e 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
 _ZN2fl4diag5linux12context_base12capture_dataEv+0030
[  1] 0x2baa65420424 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[  2] 0x2baa740ef0f5 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[  3] 0x2baa740f12ca 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258
[  4] 

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

The problem is that your design matrix is badly scaled. The eTIV values 
are much larger than the group membership (value=1). Try subtracting the 
mean of the eTIV and dividing by the stddev to normalize it.



On 2/25/2022 8:07 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx 
files that I used to run the mri_glmfit command. I can upload 
the recon-all outputs of the individual samples as well, if needed. 
The files are uploaded in google drive, please access them via the 
link below.


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://drive.google.com/drive/folders/1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k?usp=sharing 



Thank you in advance,
Hyunwoo Jeong.



2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 
님이 작성:


Can you upload the data to me somewhere? I'd need the input volume
and the fsgd and any contrasts

On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이
작성:

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same
problem occurred when I ran the command with --no-pcc.
Folders and files with the same names were created. and the
following error message (identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:

It looks like it is failing when computing the partial
correlation coef. Try  running it with --no-pcc

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output
files were created.

After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was
created. In the glmdir folder,
'three_group_comparison.area' folder was created, and
the following files were also created: beta.mgh,
dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log,
rstd.mgh, rvar.mgh, sar1.mgh, surface, and Xg.dat.

In the 'three_group_comparison.area' folder, the
following files were created: C.dat, F.mgh, gamma.mgh,
maxvox.dat, sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:

Did it create the output folder and some output
files? I noticed that there is a "error: No such
file or directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file,
mtx file and the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface
area among three groups while controlling for
estimated total intracranial volume (eTIV), as
described on the Surface Based Group Analysis
tutorial 

Re: [Freesurfer] run_samseg output folder permissions error

[Koen Van Leemput]

External Email - Use Caution

This seems to have something to do with the image read/write tools in FS's
Python tools not being able to handle ushort pixel types. One way around
this would be to convert the input image into e.g., floats before calling
samseg, but for a real fix in the code I'm looking at Andrew... (?)

On Wednesday, March 9, 2022,  wrote:

> Thank you Koen,
>
> Your suggestion allowed run_samseg to run for a few minutes, but...
>
>
> daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg
> --input o_ADNI_002_S_4654__MRI-m072.nii --output T1-only
> ##--
>   Samsegment Options
> ##--
> output directory: T1-only
> input images: o_ADNI_002_S_4654__MRI-m072.nii
> modelSpecifications: {'FreeSurferLabels': [0, 165, 258, ...
>
>  process ran for an additional few minutes and then crashed with
> the following statements (Any Thoughts?) ..
>
>
> maximalDeformation=0.0750 minLogLikelihood=-0.8762
> maximalDeformation=0. minLogLikelihood=-0.8762
> appliedScaling: 1.0021
> INFO: This is an unsigined short.
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179,
> in 
> reg_only=args.reg_only
>   File 
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py",
> line 252, in segment
> initTransform=initTransform
>   File 
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py",
> line 271, in register
> initTransform=initTransform
>   File 
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py",
> line 72, in registerAtlas
> self.saveResults( savePath, worldToWorldTransformMatrix,
> imageToImageTransformMatrix )
>   File 
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py",
> line 473, in saveResults
> inputImage = fs.Volume.read(self.imageFileName)
>   File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py",
> line 103, in read
> result = bindings.vol.read(filename)
> ValueError: unknown MRI data type ID: 10
> daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$
>
>
> The image that I am trying to test with this process is a standard
> T1-weighted image from ADNI, and Freesurfer had been able to run the basic
> segmentation (-recon-all, took about four hours and ran to completion
> without errors), so I'm not sure why Samseg can't identify the "MRI data
> type".
>
> Thanks in advance for any insights you might be able to share.
>
> -Randy
>
>
>
> -Original Message-
> From: Koen Van Leemput 
> To: daedalu...@aol.com ; Freesurfer support list <
> freesurfer@nmr.mgh.harvard.edu>
> Sent: Tue, Mar 8, 2022 11:18 pm
> Subject: Re: [Freesurfer] run_samseg output folder permissions error
>
> It looks like you have an extra slash in front of the output file name, so
> you're trying to write in the root directory...
>
> On Tuesday, March 8, 2022,  wrote:
>
> External Email - Use Caution
> Dear experts,
>
> Having installed Freesurfer on WSL2, I was able to get the basic FS
> segmentation to run without error.  However, when I tried to run_samseg on
> a single T1 image, I received the following error message (permissions
> denied creating the "output folder")
>
> Is there anything in the trace (below) that provides a clue?
>
> daedalus@DESKTOP-TILLA3B:/usr/ local/freesurfer/7-dev/ subjects$
> run_samseg --input o_ADNI_002_S_4654__MRI-m072. nii --output /T1-only
> -samsegOutput/
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/7-dev/ python/scripts/run_samseg", line 67,
> in 
> os.makedirs(args. outputDirectory, exist_ok=True)
>   File "/usr/local/freesurfer/7-dev/ python/lib/python3.6/os.py", line
> 220, in makedirs
> mkdir(name, mode)
> PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'
>
>
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Re: [Freesurfer] hypothalamic nuclei question

[Iglesias Gonzalez, Juan E.]

Dear Niels,

Would it be possible to share T1w_acpc_dc_restore_1mm.nii.gz with us so we can 
try on our end?

Cheers,

Eugenio

Juan Eugenio Iglesias
http://www.jeiglesias.com





On 9 Mar 2022, at 09:16, Niels Janssen 
mailto:njans...@ull.edu.es>> wrote:


External Email - Use Caution

I am trying to run the hypothalamic subunits segmentation but I am getting an 
error message (see below).

I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei work 
fine).

This error occurs even after changing the voxel size to 1x1x1 as per the 
instructions (because this is HCP data with 0.7mm).

Thanks for your help

Niels

---
nielsj@vein:/ImageData/DataSets/HCP/3T/100206/T1w$ 
mri_segment_hypothalamic_subunits --i T1w_acpc_dc_restore_1mm.nii.gz --o test
using 1 thread
processing 1/1
Traceback (most recent call last):
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
1463, in 
main()
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
90, in main
threads=args.threads
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
164, in predict
net = build_model(path_model, model_input_shape, len(label_list))
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
577, in build_model
input_model=None)
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
750, in unet
input_model=enc_model)
  File 
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 
948, in conv_dec
last_tensor = keras.layers.concatenate([cat_tensor, last_tensor], 
axis=ndims + 1, name=name)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
 line 931, in concatenate
return Concatenate(axis=axis, **kwargs)(inputs)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
 line 952, in __call__
input_list)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
 line 1091, in _functional_construction_call
inputs, input_masks, args, kwargs)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
 line 822, in _keras_tensor_symbolic_call
return self._infer_output_signature(inputs, args, kwargs, input_masks)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
 line 862, in _infer_output_signature
self._maybe_build(inputs)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
 line 2710, in _maybe_build
self.build(input_shapes)  # pylint:disable=not-callable
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/utils/tf_utils.py",
 line 272, in wrapper
output_shape = fn(instance, input_shape)
  File 
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
 line 519, in build
raise ValueError(err_msg)
ValueError: A `Concatenate` layer requires inputs with matching shapes except 
for the concat axis. Got inputs shapes: [(None, 176, 184, 176, 24), (None, 48, 
184, 176, 480)]





--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
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[Freesurfer] hypothalamic nuclei question

[Niels Janssen]

External Email - Use Caution

I am trying to run the hypothalamic subunits segmentation but I am getting
an error message (see below).

I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei
work fine).

This error occurs even after changing the voxel size to 1x1x1 as per the
instructions (because this is HCP data with 0.7mm).

Thanks for your help

Niels

---
nielsj@vein:/ImageData/DataSets/HCP/3T/100206/T1w$
mri_segment_hypothalamic_subunits --i T1w_acpc_dc_restore_1mm.nii.gz --o
test
using 1 thread
processing 1/1
Traceback (most recent call last):
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 1463, in 
main()
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 90, in main
threads=args.threads
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 164, in predict
net = build_model(path_model, model_input_shape, len(label_list))
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 577, in build_model
input_model=None)
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 750, in unet
input_model=enc_model)
  File
"/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits",
line 948, in conv_dec
last_tensor = keras.layers.concatenate([cat_tensor, last_tensor],
axis=ndims + 1, name=name)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
line 931, in concatenate
return Concatenate(axis=axis, **kwargs)(inputs)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 952, in __call__
input_list)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 1091, in _functional_construction_call
inputs, input_masks, args, kwargs)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 822, in _keras_tensor_symbolic_call
return self._infer_output_signature(inputs, args, kwargs, input_masks)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 862, in _infer_output_signature
self._maybe_build(inputs)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py",
line 2710, in _maybe_build
self.build(input_shapes)  # pylint:disable=not-callable
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/utils/tf_utils.py",
line 272, in wrapper
output_shape = fn(instance, input_shape)
  File
"/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py",
line 519, in build
raise ValueError(err_msg)
ValueError: A `Concatenate` layer requires inputs with matching shapes
except for the concat axis. Got inputs shapes: [(None, 176, 184, 176, 24),
(None, 48, 184, 176, 480)]





-- 
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
https://secure-web.cisco.com/1k8Xn2D4J0byFyRwIbmBKVyMDjJThmhtuWNmuBVgygLkSVhxxPebqS7fYo4B7MWMirKuq5EEUt1IbYcelrWvGTKP0ZSVQ13IzPa6F-bBFGyDEVco097MGKGNKimELqErooVe13creAe1LKe_UOvX3wUVBkQ4wW7ehVp5SyN9tNsrJx4hmqUrlCRdvBGMaTpXov2G4O0n_6wIHKxDc1DGbEjq6X4kwYm8jVenxYxX29kYRjlAtOqrWGTfei3bbznPzC3Gb7y4onNieR0gmEMKSe9iBy5f5AQAw2DtWTFwU-_pEAcUaHXGgRxd-9Z4L7Cv1/https%3A%2F%2Fsites.google.com%2Fview%2Fnielsjanssen%2F
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Re: [Freesurfer] Linear mixed model for longitudinal data

[Diers, Kersten /DZNE]

External Email - Use Caution

Hi Julian,

please see my responses below.

Best, Kersten

Am 04.03.2022 um 14:11 schrieb Julian Macoveanu 
mailto:julian.macove...@gmail.com>>:

   External Email - Use Caution

(Apologies for reposting due to lack of answer)

Dear all,

This is my first attempt to analyze longitudinal structural data with
freesurfer, and I just do my best to follow the tutorial. I have some
things not clear, so any help would be appreciated.

We have a longitudinal study design with 2 groups, healthy and
patients who were scanned at baseline a second time following a
variable time interval (6 to 36 months). We want to investigate
whether the patient’s cortical thickness/volume progresses differently
compared to controls (group-by-time interaction effects). I chose to
analyze the data with LME due to variable follow-up time, having only
50% of the patients with a second scan, and also having family members
within and between groups.

Questions
1) To account for familial relationship, should I add a family ID as
covariate that stays in the design matrix X and count this covariate
as random effect when the model is fitted? Like this:
lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere);

Where the first 3 covariates in X are counted as random effects: 1 the
intercept, 2 follow-up time and 3 family ID.

The X would further include group, age, sex, TIV, and group*time, the
last one being the interaction term we want to assess using CM.C = [0
0 0 0 0 0 0 1].

Does the X and CM look good to address our research question?

This is a three-level model, right? Time within patients, and patients within 
families - correct me if I am wrong.

In general, including ‚family‘ as a random effect is plausible in my eyes.

However, I have to admit that I am not sure at the moment how the lme tools 
handle these higher-level (i.e. more than two levels) models, in particular if 
nested random effects (patients within families) as opposed to crossed random 
effects are present.

So if it is scientifically justifiable to leave out ‚family‘ as a random 
effect, you have a simpler, two-level model and are on the safe side. 
Otherwise, if you’d like to stick with the more complex model, I’d need to take 
a closer look, and it may not be supported by the toolbox.

Beyond that, I always like to also look at the most simple model, which just 
has ‚patient‘ as the single random effect (i.e. assuming parallel slopes within 
groups in your case). It may give more stable estimates, in particular for 
small samples.

Apart from these considerations about which effects to include, technically X 
and CM look OK to me.

2) It is unclear to me how to perform correction for multiple
comparisons and assess what is significant. I follow this procedure
after constructing X:

[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2 3],Y,ni,lhcortex,3);
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);
lhstats = lme_mass_fit_Rgw(X,[1 2 3],Y,ni,lhTh0,lhRgs,lhsphere);
F_lhstats = lme_mass_F(lhstats,CM);
dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0):

The dvtx is not empty but has 1 value. What I don’t understand, when
constructing the sig.mgh map it appears the FDR2 correction info is
not used:
fs_write_fstats(F_lhstats,mri,'sig.mgh','sig');

Yes, your intuition is correct, the ’sig.mgh’ file contains uncorrected 
p-values.

How can I be sure when I import sig.mgh in Freeview I only look at the
vertexes surviving multiple comparisons? The sig.mgh file shows a lot
of regions when thresholded at min 1.3

There are two ways for doing the multiple comparison correction: either 
transform the p-values from uncorrected to corrected, or just transform the 
threshold, and use the adjusted threshold on the uncorrected p-values.

The second approach is described in the tutorial; maybe take a look at the very 
end (i.e., the ‚pcor‘ threshold).

3) Given a few clusters showing an interaction effect which are saved
as sig.mgh and overlaid on surface in freeview, how do I know
(visualize) what is going on in these clusters, like which of the
group means go up or down over time? (I use FS71 and tksurfer not
working). Is it here that printing out and plotting the betas (of the
interaction term) are useful for?

Yes, that is one motivation for extracting the betas. An advantage is that the 
betas will also inform about the magnitude of the effect, so this is preferred 
way in my opinion.

As an alternative, the output from the ‚lme_mass_F‘ script, e.g. the 
’F_lhstats’ structure, contains a field called ‚sgn‘, which is the sign of the 
contrast - in the simplest case just the sign of the beta. So this might be 
used as well.

4) I have a hypothesis to find differences in prefrontal cortex, at
which step would I apply a PFC mask? I have constructed a PFC.label
file by adding corresponding label files.

I would do that just prior to multiple comparison correction: You can use a 
mask for the