[Freesurfer] Surface maps of cortical thickness

[Schranzer René]

External Email - Use Caution

Hello everyone,

I have some problems with the computation of the SD of thickness maps (mgh 
file) of 10 subjects.
First I computed the average thickness map (to fsaverage) with the command:
mris_preproc --fsgd qdec/subject_list.fsgd --target fsaverage --hemi lh --meas 
thickness --out avg-lh-thickness.mgh
mri_surf2surf --hemi lh --s fsaverage --sval avg-lh-thickness.mgh --fwhm 15 
--cortex --tval avg-lh-thickness.15.mgh

Now I wanted to calculate also the thickness std mgh file. I tried this...
mris_surface_stats -surf_name fsaverage/surf/lh.white  -out_name lh_std.mgh 
-absmean lh_absmean.mgh -mean lh_mean.mgh -absstd lh_absstd.mgh 
avg-lh-thickness.15.mgh

but this calculation of the SD mgh files does not work, because I get no 
output. Is there another way to calculate the surface maps of the SD of 
cortical thickness?

Best,
René


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Re: [Freesurfer] (no subject)

[Emil H.J. Nijhuis]

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Dear Ruopeng,

I tried the UpdateFreeview

procedure below, however I received the error message:

>>
This application failed to start because it could not find or load the Qt
platform plugin "xcb"
in "".

Reinstalling the application may fix this problem.
Abort
<<

Any advice on how to solve this problem?

With best regards,

 Emil

Date: Mon, 7 Jan 2019 17:52:39 +0100
> From: "Larissa Bechtle" 
> Subject: Re: [Freesurfer] (no subject)
> To: "Freesurfer support list" 
> Message-ID:
>
>  >
>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hi Ruopeng,
>
> Thank you very much for your quick answer and advice. So I am going to
> update freeview!
> Thanks!
> Larissa
>
> Gesendet mit der WEB.DE Mail App
>
> Am 07.01.19 um 17:35 schrieb Ruopeng Wang
>
> > Hi Larissa,
> >
> > The latest development version of freeview supports drawing labels on
> > surface. You can take a look here on how to update freeview:
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> >
> > In the latest version, you can draw paths on surface and use custom fill
> > to create/edit labels, just like in tksurfer.
> >
> > Best,
> > Ruopeng
> >
> > On 1/7/19 11:22 AM, Larissa Bechtle wrote:
> > >  External Email - Use Caution
> > >
> > > Hi everybody,
> > >
> > > after finishing my group analysis I am currently trying to run a ROI
> analysis.
> > > However I have some problems/general questions.
> > > I am trying to draw a ROI on fsaverage in order to use the
> mri_label2label command afterwards.
> > > I opened Freeview, clicked on "load surface" first and then chose
> lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose
> "New ROI" (in order to crate the ROI).
> > >
> > > So is it possible to draw a ROI when focussing only on the surface?
> And if this is the case why cant I? Did I chose the wrong file?
> > > I am really thankful for any help!!
> > >
> > > Larissa
> > >
> > >
> > > ___
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> > >
> > >
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> End of Freesurfer Digest, Vol 179, Issue 11
> ***
>
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Re: [Freesurfer] On relationship between aparc+aseg.mgz and ?h.aparc.annot

[Bruce Fischl]

Hi  Yerong

the indices and names are all in the FreeSurferColorLUT.txt file. The 
indices in [1000,2000) are for lh and in [2000,3000) are rh. For example, 
2008 is ctx-rh-inferiorparietal.

cheers
Bruce


  On Tue, 8 Jan 2019, Yerong Li wrote:

>External Email - Use Caution
>
> Dear Bruce:
>
> Thank you.
>
> So my question would be if aparc+aseg.mgz is from ?h.aparc.annot and
> aparc.a2009s+aseg.mgz is from
> ?h.aparc.a2009s.annot.
>
> Then how I can find the mapping between labels in aparc+aseg.mgz to
> labels in ?h.aparc.annot?
>
>
> The labels in ?h.aparc.annot are
>06500  660700 1316060 1326300
> 1351760 2146559
>  2647065 3296035 3302420 3302560 3957880
> 3988500 3988540
>  4924360 6553700 6558940 7874740 8204875
> 9180240 9180300
>  9182740 9211105 9221140 9221340 9231540
> 1051148510542100
> 1114631011832480131457501442310014433500
> 1446422014474380
>
> they have naming:
>
> {'unknown' }
> {'bankssts'}
> {'caudalanteriorcingulate' }
> {'caudalmiddlefrontal' }
> {'corpuscallosum'  }
> {'cuneus'  }
> {'entorhinal'  }
> {'fusiform'}
> {'inferiorparietal'}
> {'inferiortemporal'}
> {'isthmuscingulate'}
> {'lateraloccipital'}
> {'lateralorbitofrontal'}
> {'lingual' }
> {'medialorbitofrontal' }
> {'middletemporal'  }
> {'parahippocampal' }
> {'paracentral' }
> {'parsopercularis' }
> {'parsorbitalis'   }
> {'parstriangularis'}
> {'pericalcarine'   }
> {'postcentral' }
> {'posteriorcingulate'  }
> {'precentral'  }
> {'precuneus'   }
> {'rostralanteriorcingulate'}
> {'rostralmiddlefrontal'}
> {'superiorfrontal' }
> {'superiorparietal'}
> {'superiortemporal'}
> {'supramarginal'   }
> {'frontalpole' }
> {'temporalpole'}
> {'transversetemporal'  }
> {'insula'  }
>
>
> The labels in aparc+aseg.mgz are from 0-2035 and most of them are under 88.
>
> And in lookup tables, labels in aparc+aseg.mgz have different naming.
>
> Do you know how to do find relationship between volumtic labels and
> surface labels?
>
> Yerong
>
> Quoting Bruce Fischl :
>
>> Hi Yerong
>>
>> the parcellations are done on the surface to generate the annot files.
>> These are then sampled into the cortical ribbon to extend the aseg so that
>> every voxel in the cortex is given a label from the corresponding annot
>> file (aparc+aseg.mgz from aparc.annot and aparc.a2009s+aseg.mgz from
>> aparc.a2009s.annot)
>>
>> cheers
>> Bruce
>>
>>
>> On
>> Tue, 8 Jan 2019, Yerong Li wrote:
>>
>>>External Email - Use Caution
>>>
>>> Dear Freesurfer experts:
>>>
>>> I am on ROI analysis tutorial:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0
>>>
>>> And I am trying to understand the relationship between:
>>>
>>>/label/?h.aparc.annot and /mri/aparc+aseg.mgz
>>>/label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz
>>>
>>> I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany
>>> atlas" and its labels have 35 different labels (except unknown 0),
>>> while in several cases you mentioned that "/mri/aparc+aseg.mgz"
>>> corresponds to "Desikan-Killiany atlas", which I DO NOT understand.
>>>"/mri/aparc+aseg.mgz" to me are subcortical segmentations while
>>> "/label/?h.aparc.annot" are cortical(surface) parcellations.
>>> "Desikan-Killiany atlas" should mean "cortical (surface)
>>> parcellations".  That's why I do not understand why
>>> "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"?
>>>
>>>  Could anyone help me understand this?
>>>
>>> Yerong
>>>
>>>
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>>>
>>>
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Re: [Freesurfer] Programs samples two surface parcellation into volumetric segmentation

[Bruce Fischl]

Hi Yerong

mri_aparc2aseg combines the aseg and the aparc to generate files like the 
aparc+aseg.mgz. You can look in the recon-all.log or recon-all.cmd file to 
see how it is run (or the help)

cheers
Bruce


On Tue, 8 Jan 2019, Yerong Li wrote:

>External Email - Use Caution
>
> Dear Freesurfer experts:
>
> In notice "mris_sample_parc" samples a volumetric parcellation onto a
> surface, I am trying to find a program that samples "annot" files to
> volumetric parcellations. I need to know the connection between labels
> in [lh.aparc.annot, rh.aparc.annot] and labels in [aparc+aseg.mgz].
>
> I am expecting a program with two inputs [lh.aparc.annot,
> rh.aparc.annot] and output [aparc+aseg.mgz]
>
> ** Basically I have fibers from tracking algorithms and I am
> reconstructing connectivity matrices on the surface parcellation,
> that's why I need the subcortical segmentation file aparc+aseg.mgz.
>
> Yerong
>
>
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>
>
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Re: [Freesurfer] Subcortical divide parcellation

[Bruce Fischl]

Hi Huifang

what is your goal? We do have tools that will generate sub-segmentations of 
some structures (thalamus, amygdala and hippocampus). These are along 
anatomical lines rather than purely geometric ones.


cheers
Bruce


On Wed, 9 Jan 2019, WANG Huifang wrote:



External Email - Use Caution

Dear freesurfer experts,


I would like to do subcortical divide parcellation, such as the hippocampus. 


By my understanding in freesurfer, the cortical parcellation can be saved as 
vertices but
subcortical parcellation is only saved as volumes. 


There are a few ways I can do the cortical divide parcellation, seems do not fit
for subcortical parcellation, such as: mris_divide_parcellation. 


Can this function also do for the subcortical regions? 

Is any other suggestion for this-subcortical divide parcellation?


Thank you so much,

Huifang


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Re: [Freesurfer] Questions About Effect Sizes in Vertexwise GLM Anlaysis

[Max Owens]

External Email - Use Caution

Hi,

I just wanted to follow up and see if there was anyone who could answer my
questions:

1. What is the unit of effect size for the gamma.mgh file created by
vertexwise GLM Analysis using mri_glmfit?

2. Based on two previous posts (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html
 and
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html)
I tried to calculate Cohen’s d in all significant clusters resulting from
clusterwise multiple comparison correction of a vertexwise GLM using
mri_glmfit. I did this by dividing the gamma.mgh file by rstd.mgh to create
a cohensd.mgh file (fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh). Then
from the output of that operation I extracted the mean value in each
significant cluster from my vertexwise analysis using mri_segstats
(mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --o
sum.dat). My understanding was that this would yield the average Cohen’s d
of each cluster. However, if it is indeed Cohen’s d the effect sizes
yielded (between .01 and .02) are so small that they should be undetectable
given my sample size (N=1104). This leads me to believe that the outputs
are not in fact the average Cohen’s d of the cluster. Can anyone provide
any clarification of what the output file of this process means?
Specifically, what is the unit of effect size?

Please let me know if I can clarify anything.

Thanks,

Max

On Fri, Dec 7, 2018 at 1:02 PM Max Owens  wrote:

> Hi Freesurfer Experts,
>
> I have two related questions about the measures of effect size that can be
> derived from a vertexwise GLM analyses conducted in Freesurfer:
>
> 1. What is the unit of effect size for the gamma.mgh file created by
> vertexwise GLM Analysis using mri_glmfit?
>
> 2. Based on two previous posts (
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html
> and
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html)
> I tried to calculate Cohen’s d in all significant clusters resulting from
> clusterwise multiple comparison correction of a vertexwise GLM using
> mri_glmfit. I did this by dividing the gamma.mgh file by rstd.mgh to create
> a cohensd.mgh file (fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh). Then
> from the output of that operation I extracted the mean value in each
> significant cluster from my vertexwise analysis using mri_segstats
> (mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --o
> sum.dat). My understanding was that this would yield the average Cohen’s d
> of each cluster. However, if it is indeed Cohen’s d the effect sizes
> yielded (between .01 and .02) are so small that they should be undetectable
> given my sample size (N=1104). This leads me to believe that the outputs
> are not in fact the average Cohen’s d of the cluster. Can anyone provide
> any clarification of what the output file of this process means?
> Specifically, what is the unit of effect size?
>
> Thanks in advance for your help!
>
> Max
>
>

-- 

Max M Owens

Postdoctoral Fellow

NERVE Laboratory

University of Vermont
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[Freesurfer] Fwd: problem with contrast in 1st-level analysis

[xi star]

External Email - Use Caution

I also tried anther task-related fMRI, which has similar parameter, list as
follow:

  0  1  16  1  move

 17  0  16  1  blank

 33  2  16  1  static

 49  0  16  1  blank

 65  1  16  1

 81  0  16  1

 97  2  16  1

113  0  16  1

129  1  16  1

145  0  16  1

161  2  16  1

177  0  16  1

193  1  16  1

209  0  16  1

225  2  16  1

241  0  16  1

to build the contrast, i use the command
mkanalysis-sess -fsd bold -analysis odd.sm5.fsaverage.lh -surface fsaverage
lh -fwhm 5 -paradigm move-vs-static.par -event-related -spmhrf 0
-refeventdur 16 -TR 2 -nconditions 2 -polyfit 2 -per-run
mkcontrast-sess -analysis odd.sm5.fsaverage.lh -contrast MTlocalizer -a 1
-c 2 -nosumconds
the contrast matrix is [1 0; 0 -1], which is correct. However, the result
still show the activation the same with move-vs-blank. Every procedure was
finished with out error. I re-run many times but met the same problem.
Any idea what might be going wrong, or what I can do to fix such a
confusing problem? Thanks!!

Best,
Star


-- Forwarded message -
From: xi star 
Date: 2019年1月9日周三 下午1:26
Subject: problem with contrast in 1st-level analysis
To: freesurfer 


Hi! FS Experts!
In the fMRI experiment, there are 2 conditions:
1#  3D picture
2#  zero disparity picture
 interleaved with fixation block (0).

To compare 3D-vs-zero disparity, I used command:
mkcontrast-sess -a 1 -c 2 -nosumconds
but the results showed more activation then expected. To find the problem, I
compared 3D-vs-fix (-a 1 -c 0), the result shows the same as 3D-vs-zero
disparity.
My question is:
why the two contrast ( [1 0; 0 -1] and [1 0] ) came to the same result? How
can I compared the two conditions?
Thanks a lot !
Yours,
Star
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[Freesurfer] Talairach Transform failure

[Daniel Ferreira]

External Email - Use Caution

Dear experts,

I am processing some data and one of my cases failed. I checked the
recon-all.log and found the following:


*#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET*
*/home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri*

* talairach_afd -T 0.005 -xfm transforms/talairach.xfm *

*ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)*

*Manual Talairach alignment may be necessary, or*
*include the -notal-check flag to skip this test,*
*making sure the -notal-check flag follows -all*
*or -autorecon1 in the command string.*
*See:*

*http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
*

*ERROR: Talairach failed!*

*Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux*

*recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at
tis 11 dec 2018 11:32:31 CET*



Next, I tried to fix the issue by using tkregister:
 tkregister2 --mgz --s tal_before --fstal

However, the Talairach volume does not load as a MOVEABLE volume.

When I check the available recon-all output I only have:

orig/001 --> looks good
rawavg --> looks good
orig --> its awful (it looks like millions of white tiny voxels on a black
background)
nu --> it is empty
transforms/talairach.xfm --> is available

I was wondering if you would know about any way to fix this?

Thank you in advance,

Dani

-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se *
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Re: [Freesurfer] mris_apply_reg failing for area/volume

[Greve, Douglas N.,Ph.D.]

I have found and fixed the problem. You will need a new version of 
mris_apply_reg from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
Copy it to $FREESURFER_HOME/bin (after making a backup copy of the one 
that is there)


On 1/7/19 2:10 PM, James Michael Roe wrote:
>
> External Email - Use Caution
>
> Thanks for the quick reply. Have sent the file to you now
>
>
> - James
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* 07 January 2019 17:42
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mris_apply_reg failing for area/volume
> What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not 
> fsaverage_sym, can you send this file to me too?
>
>
> On 1/7/19 5:21 AM, James Michael Roe wrote:
>>  External Email - Use Caution
>>
>> ​Dear freesurfer experts
>>
>> I am still unable to register RH area and volume files to the LH of a 
>> symmetrical template for a number of longitudinally processed subs. This is 
>> only the case when using the --jac flag (all run fine without).
>> There appears to be quite good correspondence (although not perfect) between 
>> whether the LONG sub fails and whether the BASE of that sub fails with the 
>> same error. Some CROSS subs also fail, though there appears to be little 
>> correspondence.
>>
>> I would greatly appreciate any help you can give me.
>>
>> To recap, the command I am running is:
>>
>> #right to left
>> mris_apply_reg \
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>> --jac
>>
>>
>> #right to right
>> mris_apply_reg \
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>> --jac
>>
>>
>> Attached is the output for one CROSS sub (with fsaverage_sym as template) 
>> and one LONG (with another symmetrical template) to show that the error is 
>> not template-specific.
>>
>>
>> Thank you in advance!
>>
>>
>> ​- James
>>
>>
>>
>> 
>> From:freesurfer-boun...@nmr.mgh.harvard.edu  
>>   on behalf of James Michael 
>> Roe
>> Sent: 12 November 2018 10:52
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>>  External Email - Use Caution
>>
>> Hi again Doug
>>
>> FYI have sent the files as requested
>>
>> James
>>
>> 
>> From:freesurfer-boun...@nmr.mgh.harvard.edu  
>>   on behalf of Greve, Douglas 
>> N.,Ph.D.
>> Sent: 08 November 2018 15:01
>> To:freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Not sure what is going on. Can you send me the input rh.area file as
>> well as lh.40tvs8ref_sym_20.sphere.reg and
>> 40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>> When it asks you for an email, usegr...@nmr.mgh.harvard.edu  and not my
>> email above
>>
>>
>>
>>
>>
>>
>> On 11/08/2018 08:21 AM, James Michael Roe wrote:
>>>   External Email - Use Caution
>>>
>>> Hi Doug
>>>
>>> Here is the output file
>>>
>>>
>>> James Michael Roe
>>> PhD. Candidate
>>> Center for Lifespan Changes in Brain and Cognition
>>> Department of Psychology
>>> University of Oslo
>>> PB 1094 Blindern
>>> 0317 Oslo
>>> Mobile: 958 49 437
>>>
>>> 
>>> From:freesurfer-boun...@nmr.mgh.harvard.edu  
>>>   on behalf of Greve, Douglas 
>>> N.,Ph.D.
>>> Sent: 07 November 2018 19:02
>>> To:freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>>
>>> Can you send the terminal output that includes the error?
>>>
>>> On 11/06/2018 06:36 PM, James Michael Roe wrote:
External Email - Use Caution

 Hi Bruce

 I realise that my last message made it sound as though the problem was 
 fixed.
 However, I was only confirming that the files load fine in freeview (are 
 not corrupted) as asked.
 The issue of many subs area and volume files failing to register when 
 using --jac is still unsolved

 Appreciate the support.

 Thanks

 James

 
 From: James Michael Roe
 Sent: 31 October 2018 19:45
 To: Freesurfer support list
 Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

 Hi Bruce

 Can confirm that both files (rh.area & rh.volume) load fine in freeview

 Thanks for the help!

 James
 
 From:freesurfer-boun...@nmr.m

Re: [Freesurfer] problem with contrast in 1st-level analysis

[Greve, Douglas N.,Ph.D.]

did you look at the zero-disparity vs fixation contrast? Can you send 
your paradigm file? Can you send pictures?

On 1/9/19 12:26 AM, xi star wrote:
>
> External Email - Use Caution
>
> Hi! FS Experts!
> In the fMRI experiment, there are 2 conditions:
> 1#  3D picture
> 2#  zero disparity picture
>  interleaved with fixation block (0).
>
> To compare 3D-vs-zero disparity, I used command:
> mkcontrast-sess -a 1 -c 2 -nosumconds
> but the results showed more activation then expected. To find the 
> problem, I compared 3D-vs-fix (-a 1 -c 0), the result shows the same 
> as 3D-vs-zero disparity.
> My question is:
> why the two contrast ( [1 0; 0 -1] and [1 0] ) came to the same 
> result? How can I compared the two conditions?
> Thanks a lot !
> Yours,
> Star
>
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Re: [Freesurfer] Yeo labels

[Thomas Yeo]

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Hi Duygu,

I don't think that's the case at this moment. We usually use the following
command:

mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot

Thanks,
Thomas

On Wed, Jan 9, 2019 at 9:25 AM Tosun, Duygu  wrote:

> External Email - Use Caution
>
> Is there a recon-all flag similar to -label_v1 or -ba-labels to
> automatically create label and stat files for Yeo network parcellations?
>
>
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Re: [Freesurfer] problem with contrast in 1st-level analysis

[xi star]

External Email - Use Caution

Hi, Doug
I find two mistakes which may affect the final output after going through
FSFAST tutorial again.
first, the onset time of each block is wrong. the *original *parameter file
is
0 1 16 1 3D
17 0 16 1 FIXATION
33 2 16 1 ZERO-DISPARITY
49 0 16 1 FIXATION
65 1 16 1
81 0 16 1
97 2 16 1
113 0 16 1
129 1 16 1
145 0 16 1
161 2 16 1
177 0 16 1
193 1 16 1
209 0 16 1
225 2 16 1
241 0 16 1
the onset time was plus one seconds and the parameter file *should be
changed as*:
0 1 16 1 3D
16 0 16 1 FIXATION
32 2 16 1 ZERO-DISPARITY
48 0 16 1 FIXATION
64 1 16 1
80 0 16 1
96 2 16 1
112 0 16 1
128 1 16 1
144 0 16 1
160 2 16 1
176 0 16 1
192 1 16 1
208 0 16 1
224 2 16 1

240 0 16 1
Second, I converted the dicom file into 4D file (f.nii.gz) mistakenly,
which may also causing the wrong output. Thus, I'm trying to re-run the
data.
* Another question with tksurfer-sess:*
when I try to visualized the 1st-level analysis output, using the command:
tksurfer-sess -s sess01 -analysis stereozero.sm5.rh -c stereo-vs-zero
However, the tksurfer tool use the left hemisphere to process the data.
when i used the command:
ksurfer-sess -s sess01 -analysis stereozero.sm5.lh -c stereo-vs-zero
the tksurfer tool process the data with right hemi.
Everything went will just before several hours ago. I found a similar
question in the Mail Archive and you relpied that may be an display issue.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45045.html
How can I solve this problem?
thank you for your help!
best,
star
The message i got from the terminal:

 tksurfer-sess -s sess01 -analysis stereozero.sm5.rh -c stereo-vs-zero

Surface fsaverage lh

Map Surface fsaverage lh

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

Darwin yushandeMacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu
Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

Thu Jan 10 13:49:38 CST 2019

/Applications/freesurfer/bin/tksurfer


list stereo-vs-zero

con/map stereo-vs-zero
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/stereo-vs-zero/sig.nii.gz

maplist
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/stereo-vs-zero/sig.nii.gz

mri_concat
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/stereo-vs-zero/sig.nii.gz
--o
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii

ninputs = 1

Checking inputs

nframestot = 2

Allocing output

Done allocing

nframes = 2

Writing to
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii

cd /Users/yushanzhou/Documents/data/anatomical_data/stereo_zero

setenv SUBJECTS_DIR /Users/yushanzhou/Documents/data/anatomical_data

tksurferfv fsaverage lh inflated -overlay
/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii
-annot aparc -surf white -surf pial -fminmax 2 4


Contrasts

0 stereo-vs-zero



freeview -f
/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.pial:curvature=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.curv:visible=0:annot=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii:overlay_threshold=2,4
/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.white:curvature=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.curv:visible=0:annot=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii:overlay_threshold=2,4
/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.inflated:curvature=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/surf/lh.curv:annot=/Users/yushanzhou/Documents/data/anatomical_data/fsaverage/label/lh.aparc.annot:edgethickness=0:annot_outline=1:overlay=/Users/yushanzhou/Documents/data/anatomical_data/stereo_zero/sess01/bold/stereozero.sm5.rh/tksconcat.nii:overlay_threshold=2,4
-viewport 3d

cached.

cached.

cached.

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cached.

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reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

cached.

cached.

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

cached.

cached.

cached.

cached.

cached.

cached.

cached.

cached.

cached.

cached.

cached.

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/