Re: [Freesurfer] Qdec vertex-wise clustering question

[Douglas N. Greve]

I think i'm misunderstanding your question. Typically, you are running 
the stats on the thickness, so of course anything that changes thickness 
would impact the stats. Am I missing something?

On 7/15/2021 2:34 PM, Alejandro Meruelo wrote:
>  External Email - Use Caution
>
> I see, thank you. Would statistics on cortical thickness calculations
> be impacted?
>
> Many thanks again,
> Alejandro
>
> On Thu, Jul 15, 2021 at 8:38 AM Douglas N. Greve  
> wrote:
>> if you are doing statistics on the surface measures, then they will
>> impact the calculations
>>
>> On 7/14/2021 7:07 PM, Alejandro Meruelo wrote:
>>>   External Email - Use Caution
>>>
>>> This is very helpful, thank you! Do the recon-all generated FreeSurfer
>>> data (e.g., surfaces) impact any of the statistical calculations or
>>> are they primarily used for figure generation for Qdec?
>>>
>>> Many thanks again,
>>> Alejandro
>>>
>>> On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
>>> wrote:
 Not sure I know what you mean. For creating the design matrix, it uses
 the info from the qdec table. BTW, qdec is deprecated.

 On 7/12/2021 5:27 PM, Alejandro Meruelo wrote:
>External Email - Use Caution
>
> Hello,
>
> I had a brief question regarding Qdec vertex-wise clustering. Does
> Qdec use the data in the raw imaging files or the qdec.tables.dat file
> to generate the
> vertex-wise clustering results for cortical thickness group
> comparisons?
>
> Many thanks for your assistance,
> Alejandro
>
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Re: [Freesurfer] Qdec vertex-wise clustering question

[Alejandro Meruelo]

External Email - Use Caution

I see, thank you. Would statistics on cortical thickness calculations
be impacted?

Many thanks again,
Alejandro

On Thu, Jul 15, 2021 at 8:38 AM Douglas N. Greve  wrote:
>
> if you are doing statistics on the surface measures, then they will
> impact the calculations
>
> On 7/14/2021 7:07 PM, Alejandro Meruelo wrote:
> >  External Email - Use Caution
> >
> > This is very helpful, thank you! Do the recon-all generated FreeSurfer
> > data (e.g., surfaces) impact any of the statistical calculations or
> > are they primarily used for figure generation for Qdec?
> >
> > Many thanks again,
> > Alejandro
> >
> > On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
> > wrote:
> >> Not sure I know what you mean. For creating the design matrix, it uses
> >> the info from the qdec table. BTW, qdec is deprecated.
> >>
> >> On 7/12/2021 5:27 PM, Alejandro Meruelo wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Hello,
> >>>
> >>> I had a brief question regarding Qdec vertex-wise clustering. Does
> >>> Qdec use the data in the raw imaging files or the qdec.tables.dat file
> >>> to generate the
> >>> vertex-wise clustering results for cortical thickness group
> >>> comparisons?
> >>>
> >>> Many thanks for your assistance,
> >>> Alejandro
> >>>
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Re: [Freesurfer] /usr/pubsw reference in 7.1.1

[Drucker, Daniel]

I should add - the tksurfer call is from within 
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLICA . Is there an updated version that 
doesn’t have this issue?



On Jul 15, 2021, at 10:20 AM, Drucker, Daniel 
mailto:ddruc...@mclean.harvard.edu>> wrote:

When running tksurfer in 7.1.1 (from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz
 ) , I get:

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

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1

This probably means that Tix wasn't installed properly.



What should I do about this?

It works under 6.0.1.




--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School


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Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction

[Douglas N. Greve]

The FIR analysis can only be used with a task. It sounds like you want 
to deconvolve the HRF with the pupil diameter? This can be done, but it 
is tricky (can't  just use FIR).  You'd have to create a special task 
regressor where you have multiple columns. The first column would be the 
current task regressor. The next column would be the current regressor 
shifted down one (put a 0 in the first slot). Keep adding regressors to 
cover about 20-26 seconds (each regressor covers one TR). Then the beta 
values for these regressors will be the FIR you want. To visualize, 
you'd have to set up an F contrast (mkcontrast-sess), and then load the 
ces.nii.gz file



On 7/12/2021 6:55 AM, Doll, Laura wrote:


External Email - Use Caution

Hi,


Back in February I already had some issues with FIR analysis using a 
task regressor. In the meantime, I switched to other analysis. But now 
we would want to try that again.
I attached the old mails below, but since the problem slightly 
changed, I'll describe them again:


I want to run an analysis with the normalized pupil size as task 
regressor. Because the pupil dilation response itself is already slow 
(peaking after ~1s), we thought it would be good to use FIR instead of 
assuming a certain shape of HRF.



I tried two different analysis:

1) mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 
5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run 
-taskreg PupPAvg 1



2) same with "-event-related -nc 2 -paradigm paradigm.txt" instead of 
-notask.



With 1), the analysis does run without errors but I don't get to see a 
time course when plotting with tksurfer-sess and I don't know what 
exactly is plotted than (the maximum or the first time point or...?).


With 2) I arrive at a similar point as in February: when I try to plot 
the results, I get this error:



ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h


The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and 
rename the copy to h.nii.gz, tksurfer-sess opens including the time 
course viewer. But this shows does not show a time course.



So the question is:
How do I get time courses for this FIR analysis with a task regressor? 
Where is my mistake?




And a slightly off-topic question regarding task regressors & slice 
timing:



As far as I know, stc shifts all slices to TR/2 and with the default 
stimulus delay parameter, TR/2 is also added to the times in paradigm 
files.
But how does it work for task regressors? Do I have to give 
"corrected" values?
I.e. in my case I average the pupil size over TR in order to arrive at 
the desired number of time points. 
But should I do that around the original start of the sequence or 
around the "corrected" time (i.e. +TR/2)?



Many thanks in advance,


Laura




On 2/5/2021 2:08 AM, Doll, Laura wrote:

External Email - Use Caution Hi Doug, Thanks for your
response. No, I did not demean the task regressor... do I have to?

Yea, probably a good idea

Exactly. When I try to run tksurfer-sess, it complains about the
missing file "h". When I rename the "h-offset" file to "h", I can
run tksurfer-sess and I do see a map. The time course viewer opens
as well but it only shows one time point. 

Not sure here (have not run FIR in a long time). I noticed that you 
have -notask on your mkanalysis command. Have you tried it without 
-notask?


I can also continue to run the group analysis. During
"isxconcat-sess" it while again complain about the missing file
but mri_glmfit and following commands still work. So I do get a
group map but I am not sure what it shows. 

Depends on the contrast, but I think it should create maps for each 
time point in the FIR window.


Best, Laura

Did you demean the task regressor? Is the problem that you cannot
run tksurfer-sess? Or are you reporting multiple problems?

On 2/3/2021 8:32 AM, Doll, Laura wrote: External Email -
Use Caution Hi everyone, Is it possible to do an FIR analysis
using a task regressor instead of (or additional to) a paradigm
file? More precisely, we want to use pupil size as task regressor.
It was recorded during an auditory detection task (event related).
This works when I use "-spmhrf" or other HRF options. However, for
FIR I cannot get the expected time course in the single subjects
data. Tksurfer ends with an error because it cannot find the file
h.nii.gz: ERROR: could not determine file for
[...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist,
there is only one called "h-offset". The commands I used until
that point are (here neglecting the original task, but using
-event-related etc instead of no task results in the same error):
mkanalysis-sess   -fsd bold -stc up -surface fsaverage lh -fwhm 5
-notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run
-taskreg Pupil 1 selxavg3-sess -s S01_3 

Re: [Freesurfer] question about longitudinal data analyses

[Douglas N. Greve]

For A-TP1-vs-B-TP1, you just create a contrast (not a variable in the 
FSGD). The design matrix from your FSGD will have 6+4=10 regressors. The 
contrast for A-TP1-vs-B-TP1 would then be

1 -1 0 0 0 0 0 0 0 0
This computes the difference between Class A-TP1 and B-TP1


On 7/13/2021 11:07 AM, Ritobrato Datta wrote:


External Email - Use Caution

Good morning Doug,

I am trying to create a contrast matrix (also attached as a text file) 
for the following conditions -


I have two treatment arms A and B
For treatment arm A, I have subjects 1, 2, 3 imaged at TP1, TP2, TP3
For treatment arm B, I have subjects 4, 5, 6 imaged at TP1, TP2, TP3.

I have used the repeated measures ANOVA tutorial to set up some of the 
contrasts as follows -


GroupDescriptorFile 1   






Title A-Vs-B-Long   






Class A-TP1 






Class B-TP1 






Class A-TP2 






Class B-TP2 






Class A-TP3 






Class B-TP3 






Variables 	A-TP1-vs-A-TP2 	A-TP1-vs-A-TP3 	B-TP1-vs-B-TP2 
B-TP1-vs-B-TP3 	A-TP1-vs-B-TP1 	A-TP2-vs-B-TP2 	A-TP3-vs-B-TP3

Input sub1-TP1 A-TP11   1   0   0   
Input sub2-TP1 A-TP11   1   0   0   
Input sub3-TP1 A-TP11   1   0   0   
Input sub4-TP1 B-TP10   0   1   1   
Input sub5-TP1 B-TP10   0   1   1   
Input sub6-TP1 B-TP10   0   1   1   
Input sub1-TP2 A-TP2-1  0   0   0   
Input sub2-TP2 A-TP2-1  0   0   0   
Input sub3-TP2 A-TP2-1  0   0   0   
Input sub4-TP2 B-TP20   0   -1  0   
Input sub5-TP2 B-TP20   0   -1  0   
Input sub6-TP2 B-TP20   0   -1  0   
Input sub1-TP3 A-TP30   -1  0   0   
Input sub2-TP3 A-TP30   -1  0   0   
Input sub3-TP3 A-TP30   -1  0   0   
Input sub4-TP3 B-TP30   0   0   -1  
Input sub5-TP3 B-TP30   0   0   -1  
Input sub6-TP3 B-TP30   0   0   -1  



Question 1 - My question is how do I setup the contrasts for the 
different treatment arms -


A-TP1-vs-B-TP1  A-TP2-vs-B-TP2  A-TP3-vs-B-TP3


Question 2 - Also I have age and cognitive scores for each timepoint. 
How do I add those to the contrast file ?


Thank you for the help,

Regards

Rito

On Mon, Jul 12, 2021 at 10:51 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Yes, it will work on both. If you use a table, then pass the table
with --table tablefile instead of --y

On 7/12/2021 7:54 AM, Ritobrato Datta wrote:


External Email - Use Caution

Good morning,

Thanks Doug for the answers. Quick naive question. The analyses I
want to perform are on volumetric data parcellated using aseg and
not surface data.

Does mri_glmfit work with the output of the asegstats2table or on
voxelwise FA maps ?

Many thanks

Rito

On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:



On 7/9/2021 11:44 AM, Ritobrato Datta wrote:


External Email - Use Caution

Hi All,


I have the following data –

I have 205 subjects - each subject was imaged at 3
timepoints (baseline, followup 1 and followup 2)

The 205 subjects are split in two treatment arms with 100
subjects in the first one and 105 subjects in the second one.

For each timepoint, I have created FA maps in their native
diffusion space.

I have also extracted the mean FA maps for 187 ROIs using
mri_segstats.

For each timepoint, I have saved the results as a matrix (FA
in 187 ROIs x 205 subjects) in a text file.

So I have three files for the three timepoints.

I have the age and cognitive score for each subject at each
timepoint. And their gender.

I want to answer the following questions –

 1. Do the baseline FA correlate with the corresponding
cognitive score at baseline ?


This is a straight forward group analysis, so see
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Re: [Freesurfer] mcprextreg file structure and X

[Douglas N. Greve]

The only thing that happens is that it gets demeaned. Maybe that is 
causing the confusion?


On 7/14/2021 1:43 PM, Erik Jahner wrote:


External Email - Use Caution

Dear all,

I am trying to figure out the structure of X.dat and where 
the mcprextreg parameters are in the table. It is my understanding 
that the mcprextreg is the resulting PCA on the motion to generate 
a nuisance variable for motion.


I see the following regressors clearly: my ROI, global regressor, 
PCA-wm, and PCA-csf. There are however, additional columns none of 
which line up with the mcprextreg file for that participant. Can 
someone explain how the mcprextreg file gets processed and entered 
into the X.dat file with it is used as a nuisance regressor? I have 
also checked the fmcpr.mcdat but I also cannot find this in the X.dat 
data set



~Erik Jahner



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Re: [Freesurfer] Qdec vertex-wise clustering question

[Douglas N. Greve]

if you are doing statistics on the surface measures, then they will 
impact the calculations

On 7/14/2021 7:07 PM, Alejandro Meruelo wrote:
>  External Email - Use Caution
>
> This is very helpful, thank you! Do the recon-all generated FreeSurfer
> data (e.g., surfaces) impact any of the statistical calculations or
> are they primarily used for figure generation for Qdec?
>
> Many thanks again,
> Alejandro
>
> On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
> wrote:
>> Not sure I know what you mean. For creating the design matrix, it uses
>> the info from the qdec table. BTW, qdec is deprecated.
>>
>> On 7/12/2021 5:27 PM, Alejandro Meruelo wrote:
>>>   External Email - Use Caution
>>>
>>> Hello,
>>>
>>> I had a brief question regarding Qdec vertex-wise clustering. Does
>>> Qdec use the data in the raw imaging files or the qdec.tables.dat file
>>> to generate the
>>> vertex-wise clustering results for cortical thickness group
>>> comparisons?
>>>
>>> Many thanks for your assistance,
>>> Alejandro
>>>
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Re: [Freesurfer] /usr/pubsw reference in 7.1.1

[Douglas N. Greve]

you can use tksurferfv -- this runs freeview but with tksurfer arguments

On 7/15/2021 10:50 AM, Fischl, Bruce wrote:


Hi Daniel

Tksurfer has been deprecated for a long time. Have you tried freeview 
instead?


Cheers

Bruce

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

*Sent:* Thursday, July 15, 2021 10:21 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] /usr/pubsw reference in 7.1.1

When running tksurfer in 7.1.1 (from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz 
 ) 
, I get:


Tcl_Init failed: Can't find a usable init.tcl in the following 
directories:


/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"

Tix_Init failed: Can't find a usable Tix Init.tcl in the following 
directories:


./library

./tix8.1

./library

./tix8.1

/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1

This probably means that Tix wasn't installed properly.

What should I do about this?

It works under 6.0.1.

--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School


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Re: [Freesurfer] /usr/pubsw reference in 7.1.1

[Fischl, Bruce]

Hi Daniel

Tksurfer has been deprecated for a long time. Have you tried freeview instead?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Drucker, Daniel
Sent: Thursday, July 15, 2021 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] /usr/pubsw reference in 7.1.1

When running tksurfer in 7.1.1 (from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz
 ) , I get:

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

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1

This probably means that Tix wasn't installed properly.



What should I do about this?

It works under 6.0.1.



--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School

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[Freesurfer] /usr/pubsw reference in 7.1.1

[Drucker, Daniel]

When running tksurfer in 7.1.1 (from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz
 ) , I get:

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

This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1

This probably means that Tix wasn't installed properly.



What should I do about this?

It works under 6.0.1.




--
Daniel M. Drucker, Ph.D.
Director of IT
McLean Hospital Imaging Center
Harvard Medical School

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Re: [Freesurfer] Freesurfer not creating specific files

[Fischl, Bruce]

Hi Lisa

Is the subject fsaverage symlinked in your SUBJECTS_DIR? Also, the argument to 
-s is typically just an identifier, not a path then and identifier. That is, it 
should be more like:

recon-all -s subid

instead of

recon-all -s imagedir/subid

I’m not sure if this is the source of your problem, but certainly recon-all is 
failing to find some of the files as it throws errors like:

SUBJECTS_DIR/dfs6/pub/ltaylor2/downs
FREESURFER_HOME /data/opt/apps/freesurfer/6.0.1
Loading source label.
Invalid argument
ERROR reading /dfs6/pub/ltaylor2/downs/fsaverage/label/lh.BA1_exvivo.label

So check to see if /dfs6/pub/ltaylor2/downs/fsaverage exists and that your 
SUBJECTS_DIR is /dfs6/pub/ltaylor2/downs. If it does not exist you can create a 
symlink from $FREESURFER_HOME/subjects/fsaverage to your SUBJECTS_DIR.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Taylor, Lisa Marie
Sent: Wednesday, July 14, 2021 11:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Taylor, Derek 
Subject: [Freesurfer] Freesurfer not creating specific files


External Email - Use Caution
Hi everyone,

I could really use some help with figuring out an issue I've been struggling 
with the last few months. It seems that when I run recon-all on over 20 of my 
participants, not all freesurfer files are created. But I am not understanding 
why, and my technical capabilities are limited. Particularly, it seems there's 
an issue reading the lh.BA1_exvivo.label.  I will attach the recon-all log file 
for any other information that it can provide.

Also, I run a script for recon-all and these are the arguments: srun 
${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all 
-hippocampal-subfields-T1 -brainstem-structures -qcache

Not sure if this is pertinent, but our HPC has been updated, but I am unaware 
if that can impact how freesurfer is run.

Thank you for any insight you can provide!

Lisa
(I previously sent an email with screen shots, but the email was waiting to be 
approved due to size)



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cannot be guaranteed to be secure or error-free as information could be 
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viruses. The sender therefore does not accept liability for any errors or 
omissions in the contents of this message, which arise as a result of e-mail 
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Re: [Freesurfer] Missing freesurfer files after running recon-all

[Paul Wighton]

External Email - Use Caution

Hi Lisa,

I think is has something to do with these lines from the log:

```
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /dfs6/pub/ltaylor2/downs; ln -s
/data/opt/apps/freesurfer/6.0.1/subjects/fsaverage; cd -

ln: failed to create symbolic link './fsaverage': File exists
```

It can't find a copy of fsaverage in SUBJECTS_DIR, so recon-all tries to
link to one, but fails because it exists. (?)

I see the recon-all argument for subject (`-s imagedir/subid`) has a '/'
character in it. That might be the cause.  The 'imagedir' should be
specified by the environment variable SUBJECTS_DIR (which it looks like is
working fine in the log)

Can you try re-running it with just `-s subid` instead of `-s
imagedir/subid`?

If that's not it, is there anything else in common with the subject names
of the ones that fail? Another strange character perhaps?

For reference, the errors are starting around here in recon-all:
https://secure-web.cisco.com/1YE2a1xj00WKbbFVqM8gIEmudSBRD1jmHutdsxIQz2yLXszyaTJKc5y7AzGn6D8MM7REaznNm8YnkkVxeI-SrSWzpXfeZzgmDZgXtNcSKhnsinWRpK83BYLMIwATgiQHNx-nvEpB6fPZrRpbmGzQycSVbS0mixfs7eJDflUGxFEObZWrrLPT5s77RUL-XKuVqiTkMPDqd6HtGVmLTXoRo-FF1MJ9iFRx_7c6JtgkIvVy3aUoeav_LmNOxlL34gb97UT71LlQBAdPUyNBj040P4g/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2F5c50f486e478108ed8ce6800b50344d31af71ac3%2Fscripts%2Frecon-all%23L4913

-Paul


On Wed, Jul 14, 2021 at 5:44 PM Taylor, Lisa Marie 
wrote:

> External Email - Use Caution
>
> Hi everyone,
>
> I could really use some help with figuring out an issue I've been
> struggling with the last few months. It seems that when I run recon-all on
> over 20 of my participants, not all freesurfer files are created. But I am
> not understanding why, and my technical capabilities are limited.
> Particularly, it seems there's an issue reading the lh.BA1_exvivo.label. I
> will attach a screenshot of a participant who has all the expected files
> vs. a participant who is missing important files. I will also attach the
> recon-all log file for any other information that it can provide.
>
> Also, I run a script for recon-all and these are the arguments: srun
> ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all
> -hippocampal-subfields-T1 -brainstem-structures -qcache
>
> Not sure if this is pertinent, but our HPC has been updated, but I am
> unaware if that can impact how freesurfer is run.
>
> Thank you for any insight you can provide!
>
> Lisa
>
> --
>
> This message may contain confidential information and is for the sole use
> of the intended recipient(s). If you are not the intended recipient, do not
> use, distribute, or copy this e-mail. Please notify the UC Irvine Health –
> Compliance and Privacy Office via email at hacomplia...@uci.edu or by
> phone 888-456-7006 immediately if you have received this e-mail in error.
> E-mail transmission cannot be guaranteed to be secure or error-free as
> information could be intercepted, corrupted, lost, destroyed, arrive late
> or incomplete, or contain viruses. The sender therefore does not accept
> liability for any errors or omissions in the contents of this message,
> which arise as a result of e-mail transmission.
> ___
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Re: [Freesurfer] Problem with mri_glmfit-sim

[juergen.haenggi]

External Email - Use Caution

Dear Douglas

thanks for the information. I will try the work around or use the precomputed 
tables.

Best
Jürgen

Am 09.07.2021 um 19:58 schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:

I think this might be a bug. You might be able to get around it by adding 
--no-perm-resid as the last option. Why are you running your own simulation 
instead of using the precomputed tables?

On 6/28/2021 1:38 AM, 
juergen.haen...@upd.unibe.ch wrote:

External Email - Use Caution

Dear Douglas

please find the terminal output and the log files attached.
when I run this command in FS 6.0.0, no error occurred

thanks in advance

cheers
Jürgen



Am 27.06.2021 um 16:49 schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:

Can you send the mri_glmfit.log file from your mri_glmfit run?
Can you run mri_glmfit-sim with --debug as the first option and capture and 
send the output?

On 6/23/2021 4:42 AM, 
juergen.haen...@upd.unibe.ch wrote:

External Email - Use Caution

Dear FS experts

I have run stats using mri_glmfit (FS 7.1.1 on Mac) with the following command

mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt 
--glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf fsaverage lh --C 
IPS_2groups.mat --cortex

and everything worked fine. When trying to run simulations with mri_glmfit-sim 
with the following command

mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 
1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25

the following error occurred

Loading y from 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
error: mri_read(): couldn't determine type of file 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
   ... done reading.
ERROR: loading y 
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force

The entire output is shown below.
I do not understand why after the —y option in the command reported by FS in 
the terminal, i.e.

mri_glmfit --C 
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx 
--sim mc-z 500 1.302 
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 --sim-sign 
abs --fwhm 14.598750 --fsgd IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods 
--mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf 
fsaverage lh white

the input file (IPS_2groups_n135_lh_thickness.10.mgh) is missed and hence the 
following option —perm-force is interpreted as input file.

How can I fix this problem?

Thanks in advance for any advise
Regards
Jürgen


---
entire output:

[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi% 
mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 
1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd 
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf 
fsaverage lh --C IPS_2groups.mat --cortex
SURFACE: fsaverage lh
log file is 
IPS_2groups_n135_Thickness_LH.glmdir/lh_mc-z.abs_500p1.3.mri_glmfit-sim.log

cd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302 
lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25

FreeSurferEnv.csh 7.1.1
Wed Jun 23 10:19:19 CEST 2021
Darwin 
upddkp224.unibe.ch
 19.6.0 Darwin Kernel Version 19.6.0: Thu May  6 00:48:39 PDT 2021; 
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
jurgenhanggi
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd 
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf 
fsaverage lh --C IPS_2groups.mat --cortex

DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.598750
nSimPerJob = 500
1/1 Wed Jun 23 10:19:19 CEST 2021
mri_glmfit --C 
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx 
--sim mc-z 500 1.302 
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 --sim-sign 
abs --fwhm 14.598750 --fsgd IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods 
--mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force