[Freesurfer] using different versions of Freesurfer?

[Lee Subin Kristine]

Hi Freesurfer team,


I have currently used version 5.3. for all my cortical parcellations of MRI 
data, but for PET images of those same subjects I used the gtmseg, 
mri_coregister, gtmpvc of the 6.0 beta version to get partial volume 
effect-corrected SUVR(standard uptake value ratios).

I am aware and heard that using different versions of Freesurfer is not 
recommended, and that any results from the developmental version should not be 
used for publication yet until it is officially released.

However I was wondering if in my case(with the commands I used above), this 
would not be such an issue.


Thanks a bunch,


Kristine
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] TRACULA Error in virtualbox

[Alexander Zent]

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined
Variable. I have looked at the answers to this question that have been
previously posted but cannot seem to remedy this problem. I'm running
freesurfer 5.3 via virtualbox on windows. I have applied for a license and
added that to the license.txt file but to no avail. Thank you and I look
forward to hearing from you.

Thanks,
Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Reconstructing cerebellum in FreeSurfer 5.3

[Alexander Zent]

Hi,
I have been trying to figure out how to extract and reconstruct the
cerebellum and possible the pons and brain stem. I have already ran
recon-all and extracted the hemispheres but cannot seem to find any
documentation on how to extract the other structures. I am running version
5.3 on Windows via VirtualBox. Thanks for you help.

-Alex
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Trouble with Two Stage Longitudinal Analysis

[Timothy Hendrickson]

FreeSurfer experts,

I am attempting to use the two stage model for longitudinal analysis,
however I keep receiving an error message that my design matrix is poorly
scaled.
I belive I have cross-checked my qdec, fsgd, design matrix, and contrast
files and they all match so  I do not think the problem is a mismatch.
I am wondering if I made some sort of mistake in my script design or design
matrix creation...

Anyway here is the command line input:

mri_glmfit --glmdir
lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X
DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y
lh.testretest.thickness-pc1.stack.fwhm10.mgh --C
age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C
DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx
--C
DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx
--C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx
--C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx
--label lh.testretest.fsaverage.cortex.label --surf fsaverage lh

The error message is attached within file
AllSite_twoStageLongitudinal_DsgnMtxErr.txt

Additionally I've included my analysis script, all timepoint qdec file,
temporal average qdec file, fsgd file, and design matrix.

-Tim


Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
Design matrix --
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   12.600   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   13.800   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   12.500   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   17.200   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   16.295   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   17.800   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   12.495   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   11.095   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   15.895   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   16.665   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   11.745   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   12.500   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   13.995;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   14.740;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   11.265   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   16.240   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   1.000   0.000   0.000   0.000   13.415   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   14.835   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   1.000   0.000   0.000   0.000   14.240   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   1.000   0.000   0.000   0.000   11.835   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   16.825   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   16.835   

[Freesurfer] Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error

[Jennifer Barredo]

Hello Freesurfer experts,

I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1
format, but am receiving the following error:

"nifti1Read(): unsupported slice timing pattern 5"

Several other users have run into this problem. In the archives, there are
a few links to dead file transfer protocols for a patch for mri_convert
that might solve my problem.  May I please have a patch for mri_convert?

I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and OSX Yosemite.

Thank you,

Jennifer

-- 
Jennifer Barredo, PhD
Staff Scientist
Providence VA Medical Center
Research Affiliate
Brown Institute for Brain Sciences
jlbarr...@gmail.com
jennifer.barr...@va.gov
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freeview -dti Display as Vectors Discrepancy

[Yendiki, Anastasia]

Hi Doug - Yes, there used to be a bug in how freeview used to interpret 
orientation info from the header of volumes loaded with the -dti option. 
Hopefully it's fixed now!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Merkitch 
[douglas_merki...@rush.edu]
Sent: Wednesday, November 23, 2016 12:37 PM
To: Freesurfer support list
Subject: [Freesurfer] Freeview -dti Display as Vectors Discrepancy

Hello experts,

I have come across what I think could be an inconsistency with how freeview 
interprets and/or displays dti data as vectors. Specifically, the x component 
seems to be inverted in freeview from freesurfer-Darwin-lion-stable-pub-v5.3.0 
as compared to fslview (version 509) AND freeview from 
freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae.

Is this a known issue with a patch available? Any insight would be greatly 
appreciated.

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freeview -dti Display as Vectors Discrepancy

[Douglas Merkitch]

Hello experts,

I have come across what I think could be an inconsistency with how freeview 
interprets and/or displays dti data as vectors. Specifically, the x component 
seems to be inverted in freeview from freesurfer-Darwin-lion-stable-pub-v5.3.0 
as compared to fslview (version 509) AND freeview from 
freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae.

Is this a known issue with a patch available? Any insight would be greatly 
appreciated.

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Multiple Frames Error

[James Wilks]

Hello,
I’ve been having a problem with recon-all lately. I’m relatively new to 
FreeSurfer and the processes that I have done in the past have been done on 
sample individualized scans in my lab and I ran into an issue once I started 
trying to run FreeSurfer on fMRI data provided by our lab. Whenever I try to 
run the command this is the generated output:

#@# MotionCor Wed Nov 23 11:01:54 EST 2016
Found 1 runs
/export/home/jawilks/Desktop/freesurfer/subjects/run_02/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/export/home/jawilks/Desktop/freesurfer/subjects/run_02/mri/orig/001.mgz has 
160 frames
Linux tykwer.engin.umich.edu 2.6.18-416.el5 #1 SMP Wed Oct 26 12:04:18 EDT 2016 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s run_02 exited with ERRORS at Wed Nov 23 11:01:57 EST 2016

The archives have not been of any help and I would greatly appreciate it if 
someone would be able to help point me in the right direction.

Thank You___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

[Martin Reuter]

Hi Antonin,

we start slightly inside as surfaces expand more easily than shrink. This way 
even for the further atrophied time points there is a higher chance that it 
will be slightly inside it’s final position. 

The mris_longitudinal_surfaces is over 11 years old and was used for testing 
other approaches back then. 

Best, Martin

> On Nov 22, 2016, at 11:24 PM, Antonin Skoch  wrote:
> 
> Dear Martin,
> 
> thank you for the explanations, and sorry, I missed your previous response.
> 
> Just I am wondering, what is the reason of the shrinkage? Why not to start 
> directly from pial surface of the base?
> 
> And, I also found a binary mris_longitudinal_surfaces, which is, however, not 
> used in recon-all. What is the significance of this binary?
> 
> Antonin
> 
> ---
> 
> Hi Antonin, 
> 
> max does not constrain thickness. The location of the max is constrained to 
> be within 2*max for every iteration, so it will constrain how far outwards it 
> searches. But it will be done at each scale, so it can still deform a long 
> way.
> 
> We initialize the surface processing in long with the surface from the base. 
> But we don’t use the pial from base directly, instead we shrink it a little 
> first and start from there.
> 
> Not sure about the last question (difference between orig and prig-white 
> parameters). 
> 
> Best, Martin
> 
> 
> > On Nov 14, 2016, at 10:17 PM, Antonin Skoch  > > wrote:
> > 
> > Dear experts,
> > 
> > I am trying to understand how the pial and white surfaces are generated in 
> > longitudinal stream using information from the reconstructed base template 
> > (freeSurfer development version). 
> > 
> > In longitudinal stream, apart from the -orig, -orig_pial and -orig_white 
> > there are also parameters -long and -max 3.5.
> > 
> > May I ask what is the significance of these parameters?
> > 
> >  -max 3.5 means constraining cortical thickness to 3.5 mm? Why this 
> > constraint is applied specifically in longitudinal stream?
> > 
> > In mris_make_surfaces.c I found that -long means that initial pial vertex 
> > positions are set between final white and orig pial, slightly inside 
> > orig_pial. What is the significance of this setting in longitudinal stream?
> > 
> > Last question, not related specifically to longitudinal stream: What is the 
> > difference between -orig and -orig_white parameters of mris_make_surfaces? 
> > From the reading of source codes (quite tough to me) I got an impression 
> > that from -orig the gray and white matter histogram values are computed 
> > whereas -orig_white defines initial position of the vertices in the first 
> > iteration (which, for some reasons, does not necessary has to be identical 
> > to -orig). Am I correct?
> > 
> > Regards,
> > 
> > Antonin Skoch
> > ___
> > Freesurfer mailing list
> > Freesurfer at 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Overlap parcellation

[francesca bottino]

Hello,

I’d like to ask couple of questions regarding parcellation:



First, we used  aparc.DKTatalas40.annot  implemented in Freesurfer;



1) we used the command mris_make_face_parcellation to have a first parcellation:



mri_annotation2label --subject ${subjid1} --hemi lh --annotation 
${SUBJECTS_DIR}/${subjid1}/label/lh.aparc.DKTatalas40.annot   --outdir 
${SUBJECTS_DIR}/${subjid1}/new_label/lh

mri_annotation2label --subject ${subjid1} --hemi rh --annotation 
${SUBJECTS_DIR}/${subjid1}/label/rh.

aparc.DKTatalas40.annot --outdir ${SUBJECTS_DIR}/${subjid1}/new_label/rh


mri_convert ${SUBJECTS_DIR}/${subjid1}/func/splitted_.nii.gz 
${SUBJECTS_DIR}/${subjid1}/func/splitted_.mgz

mri_convert $d/1mm_low/aseg.mgz -o $d/aseg.mgz --reslice_like 
${SUBJECTS_DIR}/${subjid1}/func/splitted_.mgz --resample_type nearest

mris_volmask_novtk --label_left_white 2 --label_left_ribbon 3 
--label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 
$subjid1

tkregister2 --mov ${SUBJECTS_DIR}/${subjid1}/mri/T1.mgz --noedit --s ${subjid1} 
--regheader --reg ${SUBJECTS_DIR}/${subjid1}/mri/register.dat

tkregister2 --mov ${SUBJECTS_DIR}/${subjid1}/func/splitted_.mgz --noedit 
--s ${subjid1} --regheader --reg 
${SUBJECTS_DIR}/${subjid1}/mri/register_functional1.dat



P.S. splitted_.mgz  is a volume from fMRI data.



mri_label2vol --label ${f} --temp ${SUBJECTS_DIR}/${subjid1}/mri/T1.mgz 
--subject ${subjid1} --hemi ${lh_rh} --surf white  --fillthresh 0.5 --proj frac 
0 1 0.01 --o 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz 
$register_command

mri_binarize --dilate 1 --erode 1 --i 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --o 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz 
--min 1

mris_calc -o 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}_ribb_ref.nii.gz
 ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz mul 
${SUBJECTS_DIR}/${subjid1}/mri/${lh_rh}.ribbon.mgz





Is this the correct way to make the parcellation or I would need to do 
something else?

I also saw that most of the mask volumes created are overlapped each other in 
the low resolution (fMRI data) (fabout 10%) Is there any way to overcome the 
issue?




2)Then to obtain a finer parc, we have tried another method based on ico 
(icosahedron) that used as input fsaverage to create file.annot using 
mri_surf2surf that resampled one CorticalSurface onto another.This is the order 
of commands we used



mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid2ref}/surf/lh.sphere.reg 
${FREESURFER_HOME}/lib/bem/${ic}.tri 
${SUBJECTS_DIR}/${subjid2ref}/label/lh.${ic}.annot

mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid2ref}/surf/rh.sphere.reg 
${FREESURFER_HOME}/lib/bem/${ic}.tri 
${SUBJECTS_DIR}/${subjid2ref}/label/rh.${ic}.annot

mri_surf2surf --srcsubject ${subjid2ref} --trgsubject ${subjid1} --hemi lh 
--sval-annot ${SUBJECTS_DIR}/${subjid2ref}/label/lh.${ic}.annot --tval 
${SUBJECTS_DIR}/${subjid1}/label/lh.${ic}.${subjid2ref}2${subjid1}.annot

mri_surf2surf --srcsubject ${subjid2ref} --trgsubject ${subjid1} --hemi rh 
--sval-annot ${SUBJECTS_DIR}/${subjid2ref}/label/rh.${ic}.annot --tval 
${SUBJECTS_DIR}/${subjid1}/label/rh.${ic}.${subjid2ref}2${subjid1}.annot

mri_annotation2label --subject ${subjid1} --hemi lh --annotation 
${SUBJECTS_DIR}/${subjid1}/label/ rh.${ic}.${subjid2ref}2${subjid1}.annot 
--outdir ${SUBJECTS_DIR}/${subjid1}/new_label/lh

mri_binarize --dilate 1 --erode 1 --i 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --o 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz 
--min 1

mris_calc -o 
${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}_ribb_ref.nii.gz
 ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz mul 
${SUBJECTS_DIR}/${subjid1}/mri/${lh_rh}.ribbon.mgz



Is this also a  correct way to make the parcellation or I would need to do 
something else?

I also saw that, also in this case, most of the mask volumes created are 
overlapped each other in the low resolution (fMRI data) (about 10%) Is there 
any way to overcome the issue?


Thank you very much.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] QDEC versus R

[Lisa Delalande]

Hello,

As a PhD student, I send you this mail because i am meeting a misunderstanding 
with QDEC.
In a few words :

I made an analysis thanks to the QDEC tool :

  *   I tested a correlation between an inhibition score and cortical 
thickness, corrected for age

(continuous  = inhibition score ; nuisance = age ; smoothing = 25 and FDR 
corrected)


*** * ** *** * *** *** *** ** * *** 
 * ** * ** ** *



  *   then, I realised a ROI analysis. I extracted different statistic values 
from this orbito-frontal region following your wiki (aparcstat2table).

Thus, I obtained for each participant, the average value of medial 
orbitofrontal cortical thickness.

Finally, I made a multiple linear regression analysis on R software which is a 
statistical software. Surprisingly, « R », indicated that it doesn't exist any 
correlation between the right medialorbito frontal thickness values and the 
inhibition scores. I don't understand why.



Can you help shed some light on this issue ?



Yours sincerely

Marine Moyon

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.