yes, that is correct

On 12/4/2019 5:30 AM, Ferraro, Pilar wrote:
>          External Email - Use Caution
>
> Yes, absolutely, this should work! Many Thanks!
> I have just one last question concerning the colors in FreeView.
> I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) 
> after.
> The contrast matrix is 1 -1 0.
> Among the results I see blue and red regions in Freeview. Am I correct 
> assuming that blue regions are the ones where cortical thickness is reduced 
> in patients relative to HC (correcting for disease duration)?
> I just wanted to ask for a confirmation.
>
> Many thanks,
>
> Pilar
>
>
>>> Message: 2
>>> Date: Mon, 2 Dec 2019 16:06:54 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one
>>>     variable
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <c8973136-8b3d-801a-9e88-2d6b8fd39...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="windows-1252"
>>>
>>> It sounds like it would be a one-group, two-variable situation, like this
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
>>> Is that not correct?
>>>
>>>
>>> On 11/28/2019 5:24 AM, Ferraro, Pilar wrote:
>>>
>>>        External Email - Use Caution
>>>
>>> Hi,
>>>
>>> I apologize if I did not explain my issue properly.
>>> I'm interested in looking at age-related thickness reductions in 1 group 
>>> (patients), but I'd like to also account for the effect of disease duration.
>>> We can say that in my case disease duration is the nuisance factor.
>>> Briefly, I have the same issue reported in here 
>>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html),
>>>  but with only one group.
>>> How would you recommend to proceed?
>>>
>>> Many  thanks,
>>>
>>> Pilar
>>>
>>> ________________________________
>>> Message: 2
>>> Date: Wed, 27 Nov 2019 16:56:20 +0000
>>> From: "Greve, Douglas N.,Ph.D." 
>>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>>>        36
>>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
>>> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: 
>>> <fbb77a97-61b5-fac5-e2b3-0ee327e29...@mgh.harvard.edu><mailto:fbb77a97-61b5-fac5-e2b3-0ee327e29...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> what is the difference between and independent variable and a covariate?
>>>
>>> On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
>>>>         External Email - Use Caution
>>>>
>>>> Yes, I did.
>>>> But in this case I have two factors, not only one. In particular, I have 
>>>> an independent variable X and a covariate I?d like to include in the model.
>>>> How would you suggest to proceed?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Pilar
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Mon, 2 Dec 2019 16:08:08 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] fsfast no run directories
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <41b08316-678f-ff4e-aa09-86993b0c7...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> In the bold directory, it looks like you have one run directory called "1". 
>>> Change this to "001"
>>>
>>> On 11/29/2019 1:48 AM, Renew Andrade wrote:
>>>
>>>        External Email - Use Caution
>>>
>>> Dear FreeSurfer experts:
>>> I have some issues with "preproc-sess" because I cannot seem to get the 
>>> setup of the directory structure or files to connect different things(the 
>>> T1 subjects with functional bold or rest files). I have this output.
>>>
>>>
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# 
>>> preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 
>>> -fwhm 5 -per-run
>>> --------------------------------------------------------------
>>> preproc-sess logfile is log/preproc-sess.sess1.log
>>> --------------------------------------------------------------
>>> $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
>>> root
>>> setenv FREESURFER_HOME /usr/local/freesurfer
>>> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>>> Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 
>>> 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>> /home/andraderenew/Downloads/barrios/project
>>> /usr/local/freesurfer/fsfast/bin/preproc-sess
>>> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>>> vie nov 29 07:33:28 CET 2019
>>> instem   f
>>> mc   1     f fmcpr
>>> stc  1    fmcpr fmcpr.up
>>> sm   0
>>> mask 1   brain
>>> sess1 Template -----------------------------
>>> mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project 
>>> -fsd bold -update
>>>
>>> Session: /home/andraderenew/Downloads/barrios/project/sess1 ----------------
>>> vie nov 29 07:33:28 CET 2019
>>> ERROR: no run directories found
>>>
>>>
>>>
>>> my working directory is
>>>
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd
>>> /home/andraderenew/Downloads/barrios/project
>>>
>>> and
>>>
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls
>>> copy.sh  sess1   sess2  sess4  sess6  sess8  sessidlist
>>> log      sess10  sess3  sess5  sess7  sess9  sessidlist~
>>>
>>>
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls
>>> bold  rest  subjectname
>>>
>>>
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1#  cd 
>>> bold
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# 
>>> ls
>>> 1
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# 
>>> cd 1
>>> root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1#
>>>  ls
>>> sub-0030689_task-resthypnotic_bold.nii.gz
>>>
>>>
>>>
>>> And that is all. If I try with tutorial data there is no problem. One of 
>>> the obvious differences is SUBJECTS_DIR is pointing not to subjects in 
>>> freesurfer but to another folder where also is fsaverage. I don't know if 
>>> this is required or I am missing another linking file.
>>>
>>> There you can see the files I have searched with terminal.
>>>
>>> Sincerely,
>>> Andrade.
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Mon, 2 Dec 2019 16:10:20 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Problems about registration and tksurfer
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <edc3d070-848e-d108-7fc1-df9243447...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Try using mri_vol2surf to sample your fMRI onto the surface, then load it 
>>> as a surface overlay in freeview
>>>
>>> On 11/29/2019 3:35 AM, ?? wrote:
>>>
>>>        External Email - Use Caution
>>>
>>> Dear madam or sir,
>>>    I'm a student in China who use the Freesurfer to analyse my fMRI data 
>>> and overlay some results on the surface. I met some problems about 
>>> registration when I map my retinotopic results on the surface.
>>>    I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and 
>>> the sulutions are matrix, the rows are voxels and the column is polar angle 
>>> or eccentricity. So I replaced the BOLD values by the solutions in a volume 
>>> image, for example, the polar angle solution, and I used it as overlay 
>>> volume image, meanwhile I used the original volume image which is same but 
>>> BOLD value didn't been changed as the template image to register, but 
>>> whichever methods listed in the multimodal registration I used, the overlay 
>>> volume image couldn't been overlaid in correct position on the inflated 
>>> surface by freeview, just like the pic1.png in the attachment, at the same 
>>> time the overlay volume image could been overlaid on the orig surface in 
>>> correct position like the pic2.png in the attachment, so my first problem 
>>> is why the inflated surface couldn't be overlaid correctly but the orig 
>>> surface could be with the same registration data and what can I do to make 
>>> the overlay volume image overlay on the inflated surface in correct 
>>> position by freeview?
>>>   Moreover I also used tksurfer to overlay, fortunately the overlay volume 
>>> image could overlay on the inflated surface in correct position. But the 
>>> overlay color scale couldn't be color wheel like the red-green-blue. 
>>> Furthermore, the display in the tksurfer is upside down just like the 
>>> pic3.png in the attachment. So my second problem is if there are some ways 
>>> to make the tksurfer color scale like the freeview and how to make the 
>>> tksurfer display correctly?
>>>   Best regards,
>>>   Qing Zhu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Mon, 2 Dec 2019 16:12:42 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] about mri_vol2surf and mri_surf2surf
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <d49f91cf-9b15-0645-28a7-a9a557d60...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>
>>>
>>> On 11/29/2019 4:27 AM, ??? wrote:
>>>
>>>        External Email - Use Caution
>>>
>>> Hello,
>>>
>>> I have some questions about the command of mri_vol2surf and mri_surf2surf
>>>
>>> 1. For fMRI data, I find previous paper reported that they used standard 
>>> SPM8 preprocessing routines, no normalize to standard MNI152 template. The 
>>> T-map images were translated to the individual cortical surface by using 
>>> mri_vol2surf function, and then by using mri_sur2surf, all images were 
>>> translated to the fsaverage space for intersubject comparison. But for me, 
>>> I use the FsFAST to analysis our fMRI data and get each individual P-value 
>>> result about sig.nii.gz. How do I use mri_surf2surf function, for 
>>> translating to fsaverage space? Would I use the preprocessing with 
>>> fsaverage directly?
>>>
>>> It might already be on fsaverage, depending upon how you did the analysis. 
>>> What was your mkanalysis-sess command?
>>>
>>>
>>> 2. For quantitative T1 and MTV data, the pervious paper reported that they 
>>> used similar method (mri_vol2surf and mri_surf2surf).
>>>
>>> Where can I get the register.dat, when I use the mri_vol2surf function? May 
>>> I understand it estimates the the relation fMRI and T1? Would I use the 
>>> mri_vol2surf function and obtain an individual's surf data in fsaverage 
>>> space directly?
>>>
>>> Use bbregister
>>>
>>>
>>> 3. For labels, can I make a mask about the BA44 area in which structure is 
>>> simile with the file sig.nii.gz? How?
>>> Again, it depends on what space your sig.nii.gz is in. If it is in 
>>> fsaverage space, then you don't need to do anything more
>>>
>>> Best wished!
>>> Qianqian Yu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>> ------------------------------
>>>
>>> Message: 6
>>> Date: Mon, 2 Dec 2019 16:18:49 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Multiple comparison using Monte Carlo
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <c8beebe3-c9dc-6523-1b6d-dee753689...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> That will use the pre-computed ("cached") CSD files distributed with 
>>> FreeSurfer. This used 10,000 iterations.
>>>
>>> On 12/1/2019 11:34 PM, Ting Li wrote:
>>>
>>>        External Email - Use Caution
>>>
>>> Dear Freesurfer Expert:
>>>
>>> I have used the simulation code as show below:
>>>
>>>
>>> mri_glmfit-sim \
>>> --glmdir lh.gender_age.glmdir \
>>> --cache 4 neg \
>>> --cwp  0.05\
>>> --2spaces
>>>
>>> My question is how many iterations are done during this simulation? I 
>>> didn?t specify the iteration number.
>>>
>>> Why I didn?t have the csd file?
>>>
>>> Thanks a lot for your response!
>>>
>>> Best regards,
>>> Ting
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>> ------------------------------
>>>
>>> Message: 7
>>> Date: Mon, 2 Dec 2019 16:17:37 +0000
>>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Question on GLM - correlation
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <2fb25ca2-dfd3-e49e-684a-8cf439c10...@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="windows-1252"
>>>
>>> I'm not sure what you are doing here. You say that you have two continuous 
>>> variables, but there is only one in the fsgd file. The contrast has 3 
>>> items, but it would test for the offset, not the slope. Also, why do you 
>>> have --no-prune?
>>>
>>> On 11/29/2019 3:08 PM, Barletta, Valeria wrote:
>>> Dear Freesurfers,
>>> I am running glmfit to assess for correlation between y and another 
>>> continue variable across the cortex (ficvf), correcting for the effect of 
>>> age, using the command:
>>>
>>> mri_glmfit \
>>> --y {surfname_cme}.mgh \
>>> --fsgd {contrast}.fsgd \
>>> --C {contrast}.mat \
>>> --pvr ${hemi}.ficvf.mgh" \
>>> --surf fsaverage $hemi \
>>> --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \
>>> --no-prune
>>>
>>> This is my matrix:
>>> 1 0 0
>>>
>>> And my fsgd file:
>>>
>>> Title CME
>>> Class MS
>>> Variable age
>>> Input MS069_R01_01  MS  29
>>> Input MS070_R01_02_R1year  MS  44
>>> Input MS072_R01_04  MS  38
>>> Input MS073_R01_05 MS 47
>>> Input MS075_R01_07_R1year MS 34
>>> Input MS076_R01_08 MS 25
>>> Input MS077_R01_09 MS 30
>>> Input MS078_R01_10 MS 22
>>> Input MS080_R01_12 MS 52
>>> Input MS081_R01_13 MS 31
>>> Input MS082_R01_14 MS 37
>>> Input MS084_R01_16 MS 42
>>> Input MS086_R01_18 MS 28
>>> Input MS087_R01_19_R1year MS 39
>>> Input MS088_R01_20 MS 44
>>> Input MS089_R01_29 MS 44
>>> Input MS090_R01_21 MS 32
>>> Input MS091_R01_22 MS 32
>>> Input MS092_R01_23 MS 36
>>> Input MS094_R01_25 MS 47
>>> Input MS104_R01_36 MS 52
>>>
>>>
>>> This is the result:
>>> [cid:part1.9EE9F34D.23B9DFF4@mgh.harvard.edu][cid:part2.A1889CBE.3AAE2CA4@mgh.harvard.edu]
>>>
>>> Am I proceeding correctly?
>>>
>>> Thank you,
>>> Valeria
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>> ------------------------------
>>>
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>>> Freesurfer@nmr.mgh.harvard.edu
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>>>
>>> End of Freesurfer Digest, Vol 190, Issue 3
>>> ******************************************
>
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