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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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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 starxifd@gmail.com Date: 2019年1月9日周三 下午1:26 Subject: problem with contrast in 1st-level analysis To: freesurfer freesurfer@nmr.mgh.harvard.edu
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
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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Thanks for you reply. the zero-disparity vs fixation contrast is [0 1] the 3d vs zero disparity contrast is [1 0; 0 -1] the 3d vs fixation contrast is [1 0] the paradigm is as follow: 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 contrast files and visualization of the three comparisons are also in the attachment. Hope these information can help to solve the problem! thanks! best, star [image: 3d vs fix.jpeg] [image: 3d vs zero-disparity.jpeg] [image: zero-disparity vs fix.jpeg]
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 CautionHi! 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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. 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
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reading colortable from annotation file...
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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 CautionHi! 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi, Doug Apologies in advance for many basic questions in previous email. I figure out the visualization problem after correcting the command. I re-run the data using changed parameter file shown in attachment. However, the result have no change at all. The whole commands (step-by-step, lh only): preproc-sess -s sess01 -fsd bold -stc odd -surface fsaverage lhrh -fwhm 5 -per-run mkanalysis-sess -fsd bold -analysis stereozero.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm stereo-vs-zero.par -event-related -spmhrf 0 -refeventdur 16 -TR 2 -nconditions 2 -polyfit 2 -per-run mkcontrast-sess -analysis stereozero.sm5.lh -contrast stereo-vs-zero -a 1 -c 2 -nosumconds selxavg3-sess -analysis stereozero.sm5.lh -s sess01 tksurfer-sess -s sess01 -analysis stereozero.sm5.lh -c stereo-vs-zero
Can you give me some advice ？ Thanks! best, star [image: 3d_vs_zero-diaparity.jpeg] [image: zero-disparity_vs_fixation.jpeg] [image: 3d-fixation.jpeg]
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 CautionHi! 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
xi star