date:20200512

Re: [Freesurfer] Solving the Lazy Symbol binding errors

2020-05-12 Thread fsbuild

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Sorry - forgot the download link,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg

On May 12, 2020, at 23:59, fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionHello Renxi,You could 
try downloading the 6.0.0 release from here and use the installer package. 
Since the package is unsigned, you will need sudo/admin privileges to 
install it, but you should not need to disable SIP. After downloading and 
launching the installer, you will need to go into the System Preferences menu 
- Security  Privacy - and give the installer permission to run, as 
well as maybe click thru some subsequent permission prompts.-R.On May 12, 2020, 
at 23:25, RENXI LI rli...@wisc.edu 
wrote:External Email - Use 
CautionHi,I was trying to 
get through the lazy symbol binding errors and I have disable the SIP. I have 
the following errors, would you mind taking a look to see what might goes 
wrong?Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Running this will update some of your freesurfer binaries.Shall I 
proceed? [y/n/Abort]: yrsync -zbrlv --progress 
--suffix=.1589339130_bakrsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*/Applications/freesurferreceiving
 file list ...rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)0 files to considersent 4 bytes 
received 9 bytes 8.67 bytes/sectotal size is 0 speedup is 0.00rsync 
error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com..apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404)
 
[receiver=2.6.9]Best,Renxi___Freesurfer
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Re: [Freesurfer] Solving the Lazy Symbol binding errors

2020-05-12 Thread fsbuild

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Hello Renxi,
You could try downloading the 6.0.0 release from here and use the installer 
package. Since the package is unsigned, you will need sudo/admin 
privileges to install it, but you should not need to disable SIP. After 
downloading and launching the installer, you will need to go into the System 
Preferences menu - Security  Privacy - and give the installer 
permission to run, as well as maybe click thru some subsequent permission 
prompts.
-R.

On May 12, 2020, at 23:25, RENXI LI rli...@wisc.edu 
wrote:External Email - Use 
CautionHi,I was trying to 
get through the lazy symbol binding errors and I have disable the SIP. I have 
the following errors, would you mind taking a look to see what might goes 
wrong?Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Running this will update some of your freesurfer binaries.Shall I 
proceed? [y/n/Abort]: yrsync -zbrlv --progress 
--suffix=.1589339130_bakrsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*/Applications/freesurferreceiving
 file list ...rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)0 files to considersent 4 bytes 
received 9 bytes 8.67 bytes/sectotal size is 0 speedup is 0.00rsync 
error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404)
 
[receiver=2.6.9]Best,Renxi___Freesurfer
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Re: [Freesurfer] Fw: Error: Command Not Found

2020-05-12 Thread Chung, Evan R.

I’ll try emailing SimNIBS support. It’s either FSL or FreeSurfer, I wasn’t sure 
which. Thanks!

Get Outlook for iOS

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

Sent: Tuesday, May 12, 2020 11:22:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Fw: Error: Command Not Found

Is that a FreeSurfer command? I can't find it in our tree. It looks like it 
might be FSL(?).

On 5/12/2020 10:34 PM, Chung, Evan R. wrote:

From: Chung, Evan R.
Sent: Tuesday, May 12, 2020 10:30 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Error: Command Not Found

Hello Freesurfer Developers,

I'm attempting to run the command "mri2mesh --all (specific folder and files)" 
but a "command not found" error after it runs for a few minutes. I've attached 
a screenshot showing this error. I couldn't find a similar error in the list. 
I'm using Freesurfer 6.0 on macOS Catalina, and I've installed the patch. Do 
you know how I might troubleshoot this?

Best,
Evan

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Re: [Freesurfer] Compare individual to a group

2020-05-12 Thread Xiaojiang Yang

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Hi Douglas,

I have tried to follow your suggestion to use the transformed thickness file
like this:

mris_preproc --fsgd xxx.fsgd \

--meas $meas.fwhm$smoothing.xformed.mgz \

--target fsaverage \

--hemi $hemi \

--out $hemi.$meas.$smoothing.mgh

But it says $meas.fwhm$smoothing.xformed.mgz does not match surface
(163842,166904).

My files $meas.fwhm$smoothing.xformed.mgz come from
$meas.fwhm$smoothing.fsaverage (just by multiplying it with a weight). If I
use "--cache-in" in the mris_preproc like below:

mris_preproc --fsgd xxx.fsgd \

--cache-in $meas.fwhm$smoothing.fsaverage \

--target fsaverage \

--hemi $hemi \

--out $hemi.$meas.$smoothing.mgh

The above command line runs fine.

I know the problem in the first command line might be that the files
$meas.fwhm$smoothing.xformed.mgz are already on the fsaverage surface, not
the subject surface. But mris_preproc is still trying to use mri_surf2surf
to resample those mgh file from the subject surface to fsaverage surface,
which leads to the "does not match surface" error.

My question is: How can I tell mris_preproc to regard those transformed
files to be on the fsaverage surface already (instead of subject's surface),
just like the second command line where the "-cache-in" option is used?

You know, my transformed files are Just derived from cached files
$hemi.$meas.fwhm$smoothing.fsaverage.mgh in the $subject/surf directories. I
do not want to use mri_surf2surf to transform them to the subject surface
first, and then let mris_preproc transform them back to fsaverage surface
again.

Thanks!

Xiao

Douglas N. Greve
Mon, 11 May 2020 14:14:42 -0700

Just call your thickness file some other name, eg, lh.xformed.thickness.mgz,
the just specify --meas xformed.thickness.mgz

On 5/11/2020 3:52 PM, Xiaojiang Yang wrote:

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Thank you Douglas!

If I apply my transform to both the healthy controls and the patient, I
guess I would lose the convenience of using mri_glmfit, which eventually
loses the convenience of using mri-glmfit-sim (I don't care not using
mri_glmfit, but I want to use mri_glmfit-sim to do multiple comparisons
correction). That is because mri_glmfit uses the prepared output from
mris_preproc, which I have no control over to use the transformed subject.
The only way I can circumvent this is to use my transformed thickness file
to overwrite the FS calculated thickness file, but that is what I am
hesitant to do. If you have good suggestions regarding this, please let me
know. Thanks!

Xiao

On Mon, May 11, 2020 at 12:25 PM Douglas N. Greve mailto:dgr...@mgh.harvard.edu> mailto:dgr...@mgh.harvard.edu>> wrote:

I guess you could apply your transform to both the healthy
controls and to your patient, can then create an FSGD file with
two classes as before but no continuous variable. Then just have a
contrast that computes the diff between the patient and the mean
of the controls.

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Re: [Freesurfer] Fw: Error: Command Not Found

2020-05-12 Thread Douglas N. Greve

Is that a FreeSurfer command? I can't find it in our tree. It looks like 
it might be FSL(?).


On 5/12/2020 10:34 PM, Chung, Evan R. wrote:




*From:* Chung, Evan R.
*Sent:* Tuesday, May 12, 2020 10:30 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Error: Command Not Found
Hello Freesurfer Developers,

I'm attempting to run the command "mri2mesh --all (specific folder and 
files)" but a "command not found" error after it runs for a few 
minutes. I've attached a screenshot showing this error. I couldn't 
find a similar error in the list. I'm using Freesurfer 6.0 on macOS 
Catalina, and I've installed the patch. Do you know how I might 
troubleshoot this?


Best,
Evan




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[Freesurfer] Fw: Error: Command Not Found

2020-05-12 Thread Chung, Evan R.

From: Chung, Evan R.
Sent: Tuesday, May 12, 2020 10:30 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Error: Command Not Found

Hello Freesurfer Developers,

I'm attempting to run the command "mri2mesh --all (specific folder and files)" 
but a "command not found" error after it runs for a few minutes. I've attached 
a screenshot showing this error. I couldn't find a similar error in the list. 
I'm using Freesurfer 6.0 on macOS Catalina, and I've installed the patch. Do 
you know how I might troubleshoot this?

Best,
Evan

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Re: [Freesurfer] Information regarding FreeSurferColorLUT.txt

2020-05-12 Thread Douglas N. Greve

you can look in the stats folder in the recon-all output. Eg, 
aseg.stats, wmparc.stats. The ?h.aparc*.stats file are surface-based (so 
not in the LUT per se), but you can create segmentation volumes from 
them (eg, the aparc+aseg.mgz)


On 5/11/2020 10:56 PM, Safi Ullah . wrote:


External Email - Use Caution

Thank you Doug,

With reference to "There is not a single mgz file that has all of 
those segmentations, and there are some ROIs that we do not segment 
yet, substantia nigra being one of them" , is there any detail about 
the volumes/segmentation link? I mean which mgz files correspond to 
which segmentations? may be you have some documentation for that.


With reference to "Not sure, Eugenio will have to weigh in" please 
find the attached log file.


Regards,
Safi

On Tue, May 12, 2020 at 2:22 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:




On 5/10/2020 12:24 PM, Safi Ullah . wrote:


External Email - Use Caution

Dear Freesurfer,
*Q.1*: The colors of FreeSurferColorLUT.txt corresponds to which
mgz file?
I wanted to extract Substancia-Nigra but with reference to a
conversion, held in 2019,
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63560.html,
segmentation for the serial # of Substancia-Nigra is not
supported in version 6, is it supported by Version 7? if not then
i would like to write a code to extract labels for
Substancia-Nigra based on the color code (RGB). is it possible?
as the slices are in grayscale.

There is not a single mgz file that has all of those
segmentations, and there are some ROIs that we do not segment yet,
substantia nigra being one of them.

*Q.2*: I also need to extract Anterior Commissure and Posterior
Commissure.

We do not segment AC or PC yet either.

*Q.3*: While reading the brainstem-structures.log, I came
across this statement (it appears multiple times)
" * WARNING: Registration did not converge in 5 steps!
  *          Problem might be ill posed.
  *          Please inspect output manually! "
why i get this warning and how to get rid of it? because i think
the segmented midbrain does not cover the whole midbrain area.

Not sure, Eugenio will have to weigh in.


Thanks in advance

Safi

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[Freesurfer] FreeSurfer v6.0 minimal Docker image

2020-05-12 Thread Ерохин Александр

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Hello together!
 
I’d like to share my attempt on providing minimal Docker image of the 
FreeSurfer that is fully operational in terms of recon-all functionality.
 
Please see: https://hub.docker.com/r/alerokhin/freesurfer6
 
Compressed size is  732.6 MB
Size of pulled image is  1.92GB
 
Please follow simple instructions from Docker hub repository in order to get it 
running.
In case of any issues or suggestions please contact me by email specified in 
the description of the repository.
 
Really hope that it would be helpful for someone.
 
Best regards,
Aleksandr Erokhin.___
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Re: [Freesurfer] tkmedit in FreeSurfer 7.0

2020-05-12 Thread Douglas N. Greve

There is a script called tkmeditfv which runs freeview with 
tkmedit-style arguments. Most of the time, this is much easier


On 5/12/2020 3:30 PM, Hoopes, Andrew wrote:


Hi Aylin,

You can add this to your SetUpFreeSurfer script in $FREESURFER_HOME, 
but in general tkmedit is no longer supported after v6, please just 
use freeview.


Best

Andrew

*From: * on behalf of "Dincer, 
Aylin" 

*Reply-To: *FS Help 
*Date: *Monday, May 11, 2020 at 3:17 PM
*To: *FS Help 
*Subject: *[Freesurfer] tkmedit in FreeSurfer 7.0

*External Email - Use Caution *

Hi FreeSurfer Experts,

We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the 
.xdebug_tkmedit file, it outputs the following error:


“Tcl_Init returned 1: Can't find a usable init.tcl in the following 
directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4”


It looks like when we manually set the environmental variable 
TCL_LIBRARY to point to the tcl location in the $FREESURFER_HOME 
folder, tkmedit will open. Is there a way to fix this so it 
automatically sets this environmental variable?


Thanks!

Aylin

_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



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Re: [Freesurfer] tkmedit in FreeSurfer 7.0

2020-05-12 Thread Hoopes, Andrew

Hi Aylin,

You can add this to your SetUpFreeSurfer script in $FREESURFER_HOME, but in 
general tkmedit is no longer supported after v6, please just use freeview.

Best
Andrew

From:  on behalf of "Dincer, Aylin" 

Reply-To: FS Help 
Date: Monday, May 11, 2020 at 3:17 PM
To: FS Help 
Subject: [Freesurfer] tkmedit in FreeSurfer 7.0


External Email - Use Caution
Hi FreeSurfer Experts,

We are unable to use tkmedit using FreeSurfer 7.0 (centos 7).  In the 
.xdebug_tkmedit file, it outputs the following error:

“Tcl_Init returned 1: Can't find a usable init.tcl in the following 
directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4”

It looks like when we manually set the environmental variable TCL_LIBRARY to 
point to the tcl location in the $FREESURFER_HOME folder, tkmedit will open. Is 
there a way to fix this so it automatically sets this environmental variable?

Thanks!
Aylin
_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

2020-05-12 Thread Douglas N. Greve


Can you email the fsgd file?

On 5/12/2020 1:35 PM, Marina Fernández wrote:


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Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am 
running mri_glmfit.


Whenever I run an analysis in which the experimental design has more 
than 12 columns, I get the same error, whereas if the experimental 
design has less than 12 columns, the analysis is successful.


I also send you the fsgd.txt file (through FTP File Exchange). In this 
file you can see that there are four groups that have been created by 
the combination of two discrete variables (sex and apoe-type).


How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to 
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat

Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.79984   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700 0.0   
0.0   0.0  -0.73337   0.0   0.0 0.0  -0.84287   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0  -0.82284   
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0 0.0   
0.0  -0.32012   0.0   0.0   0.0 0.17882   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.33908   
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0 1.71704   
0.0   0.0   0.0   0.09313   0.0 0.0   0.0 
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.66002   0.0   0.0   0.0  -0.11350 0.0   0.0   
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.48385   0.0   0.0   0.0  -0.94000 0.0   0.0   
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.83619   0.0   0.0   0.0  -2.38637 0.0   0.0   
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.28399   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.86996   
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
1.18853   0.0   0.0   0.0   0.91963 0.0   0.0   
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871 0.0   
0.0   0.0  -0.94000   0.0   0.0 0.0   1.53105   
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0 0.0   
0.0   0.50638   0.0   0.0   0.0 0.73974   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403 0.0   
0.0   0.0   0.50638   0.0   0.0 0.0   0.23391   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0  -0.91298   
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0 
 -1.63020   0.0   0.0   0.0   0.09313 0.0   0.0   
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002 0.0   
0.0   0.0  -1.55987   0.0   0.0 0.0  -0.15173   
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0 0.0   
0.0  -0.32012   0.0   0.0   0.0 1.28564   0.0   
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0 0.30768   
0.0   0.0   0.0  -0.94000   0.0 0.0   0.0 
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
1.71704   0.0   0.0   0.0   0.50638 0.0   0.0   
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.48385   0.0   0.0   0.0  -0.52675 0.0   0.0   
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0 0.0   
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0   
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0 0.0   
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700 0.0   
0.0   0.0  -0.94000   0.0   0.0 0.0  -0.93803   
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466

[Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

2020-05-12 Thread Marina Fernández

External Email - Use Caution

Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0

[Freesurfer] mri_glmfit error

2020-05-12 Thread Marina Fernández

External Email - Use Caution

 Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0

[Freesurfer] Robust Regression with Univariate LME

2020-05-12 Thread Hua, Jessica

External Email - Use Caution

Hi FreeSurfer Experts,

There are a couple of outliers in my data.  I had winsorized the variable, but 
now I am trying to use robust regression to weight these outliers in my 
longitudinal analyses.  In Matlab there is a robustfit function. Is there a way 
to modify the lme_fit_FS code to incorporate robust regression?

Best,

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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