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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.
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. 

cached. 

cached. 

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. 

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cached. 

cached. 

cached. 

cached. 

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/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. 


Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> 于2019年1月10日周四 上午7:32写道：
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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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