[Freesurfer] Extracting significant regions - Longitudinal two stage model

[Liliana Wu]

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Hi,

I ran a longitudinal two stage model analysis in 83 participants comparing two 
groups. After applying cluster correction, I am seeing several significant 
regions, and I was wondering if there is a way to extract each significant 
cluster from each participant.

I appreciate any help!

Thank you,
Liliana

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[Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

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Hello!

I am having trouble with creating my contrast files. I did go over FsfdExamples 
(https://secure-web.cisco.com/1ezcK_pFVwJfmWpdVsJeZORU_8kaDi3SfZnw3BO98zpMkJch-p_v87YwJzoqtiefk_hIobUKYja2omqZRjod-i1GdU-HkzipUmBlo5LVsklOHdteQtjAi1L5l1J_T5iRzcE-h_C2xiFxUcjQxPmDrQFVFDP-mFdgiDx4hibkUidw4NEsFW1XHiR7roksIT1GrgvmbILffvuecnvDO6Z8oTqSldk1jddeE0vQYO5WHK19PUmdcg_uW0gtN1EgAhq3AxmE2NcKh2djkfca5f3nqamoDBZ84nG1kz_J43CQgPHPe_lX5eVqUfcsPGuqiMUbpt15_ZNoCDBTS88hFbjyFVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples).
 However, I am unsure how should I create my contrast files if I want do a 2 
group comparison while controlling 4 covariates:

Class:
Patients, healthy control

variables are:
Age,gender,episodes,residuals,


Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)
1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 (measure 
group differences while accounting for covariates)



For some reason I think I am setting up those contrast files wrong… Any help is 
appreciated.

Best,
Liliana

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

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Thank you Douglas. That’s much clearer. I do however,  have a subject without a 
gender disclosure. Would I set up my class and contrasts as:

5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa


then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?



Best,
Liliana

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[Freesurfer] TRACULA - custom tracts and path labelling

[Liliana Wu]

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Hi,

I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF)  
but I am seeing that this tract is not included in TRACULA. Does TRACULA enable 
manually selecting seed and target ROIs ?
Also, I am trying to access the list of the abbreviated names for 42 pathways 
but I don’t seem to find it. I have tried looking at 
$FREESURFER_HOME/trctrain/hcp/pathlist.txt. as suggested per tutorial.

I am new to TRACULA and I appreciate any help,

Thank you,
Liliana
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[Freesurfer] TRACULA - preprocessing error

[Liliana Wu]

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Hi,

I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am 
getting the following error
ERROR:  fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni

I don’t see the mni folder created in my files… I am trying to only reconstruct 
the following pathways.


set pathlist = ( lh.cst_JL rh.cst_JL \

  lh.unc_JL rh.unc_JL \

  lh.ccg_PP rh.ccg_PP \

  lh.cab_PP rh.cab_PP)



set ncpts = (6 6 5 5 5 5 4 4)

I appreciate any help,

Thank you
Liliana
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Re: [Freesurfer] TRACULA - preprocessing error

[Liliana Wu]

.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz 
dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz 
dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base: 
dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz 
dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz 
dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz 
dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux il-isotropic 5.4.0-122-generic #138~18.04.1-Ubuntu SMP Fri Jun 24 
14:14:03 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Aug 19 13:42:49 EDT 2022

____________
From: Liliana Wu 
Sent: August 19, 2022 12:44 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: TRACULA - preprocessing error


Hi,



I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am 
getting the following error

ERROR:  fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni



I don’t see the mni folder created in my files… I am trying to only reconstruct 
the following pathways.



set pathlist = ( lh.cst_JL rh.cst_JL \

  lh.unc_JL rh.unc_JL \

  lh.ccg_PP rh.ccg_PP \

  lh.cab_PP rh.cab_PP)



set ncpts = (6 6 5 5 5 5 4 4)



I appreciate any help,



Thank you

Liliana
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[Freesurfer] TRACULA - Ball-and-stick model fit running time

[Liliana Wu]

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Hi,

I have successfully run the preprocessing steps for my DWI data, and I was 
wondering how long does bedpostx  usually take to process DWI? I am running on 
a high-powered computer (cluster) and a multi-shell data 3 b-values of (b= 
1000s/mm2, 34 directions; b= 1600s/mm2, 45 directions; and b= 2600s/mm2, 66 
directions).

Thank you,
Liliana

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