[Freesurfer] Fwd: Re: One Group (One Factor), Two Covariates

[stdp82]

Thanks.what do I do if I would like to maintain the effect of "main" in the points 2 and 3.Best regardsStefano
 --- Begin Message ---



On 2/2/18 7:47 AM, std...@virgilio.it wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I have run:

1)

mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness 
--out rh.GROUP1.thickness.00.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 
10 --cortex --tval rh.GROUP1.thickness.10B.mgh

2)

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr 
rh.GROUP1.thickness.10B.mgh

The command line is correct?


My concern is on the fsgd file.

I have 

GroupDescriptorFile 1
Title All
Class Main
Variables thickness
Input ADNI0XX_GROUP1 Main 
Input ADNI0XY_GROUP1 Main 
Input ADNI0YX.GROUP1 Main 
...

What I should add after Main if I would like to assess the vertex by vertex 
correlation between FC (between seed and target vertex) and thickness (in the 
target vertex)?

Should I add the path where is contained rh.thickness.mgh of each subject?

Please give me an help because I did not find these information using --help or 
mail list.

Thanks


Stefano



Il 3 febbraio 2018 alle 19.55 Douglas Greve  ha 
scritto:


Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through 
the mail archives for an example on how to use it


On 2/3/18 12:10 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:

> 
> Hi list,
> 
> Is there a way to obtain a map that report the "vertex by vertex" 
> correlation between the FC (obtained by FS-FAST) and cortical thickness?
> 
> Thanks
> 
> 
> Stefano
> 
> 
> 
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> 


 

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Re: [Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

I would like to find where the functional connectivity is correlated to 
VARIABLE 1 regressing out the VARIABLE 2.

How I should set my contrast.mtx?

Thanks


Stefano

> Il 3 febbraio 2018 alle 19.57 Douglas Greve  ha 
> scritto:
> 
> 
> 
> 
> On 2/2/18 7:47 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > Hi list,
> > 
> > in reference to One Group (One Factor), Two Covariates
> > 
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > 
> > that has been applied on FS-FAST fcMRI data
> > 
> > I obtain three folder, respectively, for "main", "covariate 1", 
> > "covariate 2".
> > 
> > What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
> > each folder?
> > Please correct my conclusions if they are wrong.
> > 
> > 1 - In the "Main" folder, the sig.nii.gz contains the results of 
> > One-sample t test regressing out the effect of the two covariates.
> > 
> > > Correct
> 
> > > 
> > 2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 1 regressing out 
> > the effect for the covariate 2.
> > 
> > > Yes (and the main)
> 
> > > 
> > 3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 2 regressing out 
> > the effect for the covariate 1.
> > 
> > > Yes (and regressing out the main)
> 
> > > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > 
> > 
> > ___
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> > 
> > > 


 

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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Chris Gorgolewski]

This is not expected.

You would need to provide more details (recon-all.log) for anyone to be
able to help you. It might be also worth googling the specific error
message before hand - it could be that someone else run into this before.

Best,
Chris

On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson 
wrote:

> Since I'm following the example on the github page, using the ds005
> dataset, now with the correct license binding, I am surprised to see
> freesurfer exiting with errors (but I don't know much about freesurfer):
>
> I run this:
>
> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
> TESTING/license.txt:/license.txt:ro -v 
> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
> /bids_dataset /outputs participant --participant_label 01 02 --license_file
> /license.txt
>
> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
> 03:27:11 UTC 2018
> And then sub-02 does not run
>
> Is this what I should expect?
>
> Thanks,
>
> Dianne
>
> On Mon, Jan 22, 2018 at 9:54 PM, Dianne Patterson 
> wrote:
>
>> Wonderful...and makes total sense!  Thankyou...it is off and running now.
>> -Dianne
>>
>>
>> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
>> krzysztof.gorgolew...@gmail.com> wrote:
>>
>>> Hi Dianne,
>>>
>>> You need to "mount" the using -v the same way input and output
>>> directories are mounted. For example:
>>>
>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
>>> TESTING/license.txt:/license.txt:ro -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file /license.txt
>>>
>>> Best,
>>> Chris
>>>
>>> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson >> > wrote:
>>>
 Dear All,

 After trying the example bids app (which worked fine), I am trying the
 freesurfer bids app. I have built the docker container on my mac and I have
 the ds005 data directory here and the license.txt which I requested from
 freesurfer.
 I asked for a linux license (assuming the container contains linux and
 that was the relevant fact).

 dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
 /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
 /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
 /bids_dataset /outputs participant --license_file "license.txt"
 1: You should define 'SliceTiming' for this file. If you don't provide
 this information slice time correction will not be possible. (code: 13 -
 SLICE_TIMING_NOT_DEFINED)
 /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
 /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
 /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
 /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
 /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
 /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
 /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
 /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
 /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
 /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
 ... and 38 more files having this issue (Use --verbose to see them all).

 Summary: Available Tasks:  Available
 Modalities:
 133 Files, 1.77GBmixed-gambles taskT1w
 16 - Subjects  inplaneT2
 1 - Sessionbold


 Traceback (most recent call last):
   File "/run.py", line 165, in 
 raise Exception("Provided license file does not exist")
 *Exception: Provided license file does not exist*
 ===
 If I provide the full path to the license file, it still fails:

 docker run -ti --rm -v 
 /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
 -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
 /bids_dataset /outputs participant --license_file
 "/Volumes/Main/Working/BIDS_TESTING/license.txt"

 Suggestions?  How do I tell freesurfer where the license file is?

 Thanks so much,

 Dianne



 --
 Dianne Patterson, Ph.D.
 Research Scientist
 d...@email.arizona.edu 
 or
 dianne...@gmail.com
 University of Arizona
 Speech and Hearing Science 314
 1131 E 2nd Street, Building #71
 
 (Just East of Harvill)
 ==
 If you don't hear back from me (and you expected to),
 I blame the University's new SPAM filter.
 Please write to my gmail account.
 ==
 Antipiphany: That

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Yagmur Ozdemir 19]

Hello Dr. Greve,

The analysis.info file is below. I should also say that, when I am trying to 
create new analysis and contrast files, while creating the .config file for 
contrast, th system gives the same error saying that it cannot enter the file.

# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
# MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self 
lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
-event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 
-force
# DATE Tue Jan 30 07:14:05 EST 2018

analysis rtopyTR2.lh
mcstem fmcpr
fsd bold
TR 2
RegDOF 6
PerSession 0
RawSpace surface self lh
mask brain
RawFWHM 5
RawSTC none
nSliceGroups 1
UseB0DC 0
ApplySubCortMask 1
inorm 100
acfbins 30
fixacf  1
acffwhm 20
acfsvd  0
designtype event-related
nskip 0
polyfit 2
HPFCutoffHz 0
HeteroGCor 0
nconditions 1
parname rtopy.par
RefEventDur 10
timewindow 40.00
prestim 0
TER 0.05
gamma 2.25 1.25 2 0
stimulusdelay -1.
Condition 1 Condition01

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Saturday, February 03, 2018 9:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Strange. Can you send me the analysis.info file?


On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> Yes it exists. The output below was with debug option.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 30, 2018 8:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Does the file 
> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
> so, can you run it with -debug as the first option and send the terminal 
> output?
>
> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>
>
> Hello FreeSurfer experts,
>
> I am getting this strange error when running selxavg3-sess. (in selxavg3 
> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
> following output:
>
> #@# Sess05 ###
> /home/vm01/local/freesurfer/Project_bold/Sess05
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /home/vm01/local/freesurfer/Project_bold
> Extension format = nii.gz
> ERROR: could not open rtopyTR2.rh/analysis.info
> else
> else
> echo "--" | tee -a $LF
> echo --
> tee -a 
> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
> --
> rm $MLF
> rm /tmp/selxavg3-sess-10173.m
> if ( ! -e $okfile ) then
> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
> echo "ERROR: fast_selxavg3() failed\n" ;
> echo ERROR: fast_selxavg3() failed\n
> ERROR: fast_selxavg3() failed\n
> exit 1 ;
> exit 1
>
> The analysis folder it is referring to( rtopyTR2.rh) is in the directory from 
> which I am calling selxavg3-sess. It has the analysis.info file in which 
> doesn't have any restrictions. To troubleshoot, I moved the folder to inside 
> the session's functional directory and inside the session folder and these 
> didn't create any changes. I looked at the script and tried to debug there 
> but didn't give any results. It gave a similar error when trying to open the 
> config file of contrast in mkcontrast-sess. (I also don't have root 
> access)Any help is appreciated!
>
> Best,
> Idil
>
>
>
>
>
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>

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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Chris Gorgolewski]

This looks like a memory issue to me as indicated bu those two lines:

/opt/freesurfer/bin/reconbatchjobs: line 81:  4014 Killed
exec $JOB >> $LOG 2>&1
/opt/freesurfer/bin/reconbatchjobs: line 81:  4017 Killed
exec $JOB >> $LOG 2>&1

You can adjust how much memory of your host machine will be accessible to
your docker containers. More details here:
https://docs.docker.com/docker-for-mac/#memory

Best,
Chris

On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson 
wrote:

> Dear All,
> Pardon my ignorance.  I am trying freesurfer for the first time, using the
> BIDS docker container and the standard dataset ds005.
> Although I have specified 2 participants to run, freesurfer exits with
> errors after the first (and does the same if I run the 2nd subject
> separately).
> I am attaching the 3 logs which I take to be most relevant.  I'd be happy
> to provide other logs if they would be useful for understanding the
> problem.
> Any insight into why this is happening would be much appreciated.
>
> Thanks,
>
> Dianne
>
> On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski <
> krzysztof.gorgolew...@gmail.com> wrote:
>
>> This is not expected.
>>
>> You would need to provide more details (recon-all.log) for anyone to be
>> able to help you. It might be also worth googling the specific error
>> message before hand - it could be that someone else run into this before.
>>
>> Best,
>> Chris
>>
>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson 
>> wrote:
>>
>>> Since I'm following the example on the github page, using the ds005
>>> dataset, now with the correct license binding, I am surprised to see
>>> freesurfer exiting with errors (but I don't know much about freesurfer):
>>>
>>> I run this:
>>>
>>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_TES
>>> TING/license.txt:/license.txt:ro -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --participant_label 01 02 --license_file
>>> /license.txt
>>>
>>> A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
>>> 03:27:11 UTC 2018
>>> And then sub-02 does not run
>>>
>>> Is this what I should expect?
>>>
>>> Thanks,
>>>
>>> Dianne
>>>
>>>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> d...@email.arizona.edu 
> or
> dianne...@gmail.com
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> 
> (Just East of Harvill)
> ==
> If you don't hear back from me (and you expected to),
> I blame the University's new SPAM filter.
> Please write to my gmail account.
> ==
> Antipiphany: That moment when you realize how little you actually know
> ==
>
> --
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe from this group and stop receiving emails from it, send an
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> To view this discussion on the web visit https://groups.google.com/d/ms
> gid/bids-discussion/CAGpV9FLRhSNGsnkv%2BcJHYU_NO3rFc7iPuvf9L
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> 
> .
>
> For more options, visit https://groups.google.com/d/optout.
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Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Dianne Patterson]

Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that
makes it happy.

-Dianne

On Sun, Feb 4, 2018 at 10:52 AM, Chris Gorgolewski <
krzysztof.gorgolew...@gmail.com> wrote:

> This looks like a memory issue to me as indicated bu those two lines:
>
> /opt/freesurfer/bin/reconbatchjobs: line 81:  4014 Killed
>   exec $JOB >> $LOG 2>&1
> /opt/freesurfer/bin/reconbatchjobs: line 81:  4017 Killed
>   exec $JOB >> $LOG 2>&1
>
> You can adjust how much memory of your host machine will be accessible to
> your docker containers. More details here: https://docs.docker.com/
> docker-for-mac/#memory
>
> Best,
> Chris
>
> On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson 
> wrote:
>
>> Dear All,
>> Pardon my ignorance.  I am trying freesurfer for the first time, using
>> the BIDS docker container and the standard dataset ds005.
>> Although I have specified 2 participants to run, freesurfer exits with
>> errors after the first (and does the same if I run the 2nd subject
>> separately).
>> I am attaching the 3 logs which I take to be most relevant.  I'd be happy
>> to provide other logs if they would be useful for understanding the
>> problem.
>> Any insight into why this is happening would be much appreciated.
>>
>> Thanks,
>>
>> Dianne
>>
>> On Sun, Feb 4, 2018 at 8:43 AM, Chris Gorgolewski <
>> krzysztof.gorgolew...@gmail.com> wrote:
>>
>>> This is not expected.
>>>
>>> You would need to provide more details (recon-all.log) for anyone to be
>>> able to help you. It might be also worth googling the specific error
>>> message before hand - it could be that someone else run into this before.
>>>
>>> Best,
>>> Chris
>>>
>>> On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterson 
>>> wrote:
>>>
 Since I'm following the example on the github page, using the ds005
 dataset, now with the correct license binding, I am surprised to see
 freesurfer exiting with errors (but I don't know much about freesurfer):

 I run this:

 docker run -ti --rm -v /Volumes/Main/Working/BIDS_TES
 TING/license.txt:/license.txt:ro -v 
 /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
 -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
 /bids_dataset /outputs participant --participant_label 01 02 --license_file
 /license.txt

 A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
 03:27:11 UTC 2018
 And then sub-02 does not run

 Is this what I should expect?

 Thanks,

 Dianne


>>
>>
>> --
>> Dianne Patterson, Ph.D.
>> Research Scientist
>> d...@email.arizona.edu 
>> or
>> dianne...@gmail.com
>> University of Arizona
>> Speech and Hearing Science 314
>> 1131 E 2nd Street, Building #71
>> 
>> (Just East of Harvill)
>> ==
>> If you don't hear back from me (and you expected to),
>> I blame the University's new SPAM filter.
>> Please write to my gmail account.
>> ==
>> Antipiphany: That moment when you realize how little you actually know
>> ==
>>
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-- 
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu 
or
dianne...@gmail.com
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==
Antipiphany: That moment when you realize how little 

[Freesurfer] Removing labels after extending parcellation into white matter

[Michiko H.]

Hi Freesurfer experts,

I am wondering if it is possible to remove the original labels after
extending the parcellation by 2mm into the WM for tractography? I don't
wish to have tractography run on both sets of labels considering the
algorithm would take into account the streamlines terminating at nodes
defined by the labels so it doesn't quite make sense to count streamlines
terminating at both the original label separately from the new label
extending into the WM.

I used the following command for growing the parcellation into WM:

mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm
--hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz


Would appreciate help and suggestions!


Thanks,

Michiko.
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