Re: [Freesurfer] 3dClustSim and Gaussian filter width
Thanks Doug. I located the fwhm.dat file in my qdec output folder for the analysis I'm interested in. I see only one number (13.990453) in this .dat file, I was expecting three numbers corresponding to x, y, z directions. Do I assume this is isotropic then, that is: 13.990453 x 13.990453 x 13.990453? On Mon, Nov 30, 2015 at 11:23 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > look in the glmfit output folder for a file called fwhm.dat > > > > On 11/29/15 3:06 PM, Emma Thompson wrote: > > Sorry for the repost of my last post, but I now realize that what I need > is the estimated filter width that was actually used in the qdec analysis > not the fwhm that I actually specified, i.e. 10 mm > > > > http://afni.nimh.nih.gov/afni/community/board/read.php?1,66182,66190#msg-66190 > > > On Sun, Nov 29, 2015 at 2:51 PM, Emma Thompson <vonecono...@gmail.com> > wrote: > >> Dear Freesurfers, >> I am reposting my message in hopes that someone will reply this time >> around - still grappling with this problem. Thanks. >> >> >> >> On Tue, Oct 27, 2015 at 8:59 AM, Emma Thompson < <vonecono...@gmail.com> >> vonecono...@gmail.com> wrote: >> >>> Dear Freesurfers, >>> I am trying to use 3dclustsim in AFNI to determine the minimum number of >>> voxel in a cluster to reach significance, my understanding is that in the >>> command line the -fwhm s flag refers to the gaussian filter width and NOT >>> the Gaussian Kernel, can anyone point me to how I might be able to obtain >>> this for each hemisphere in freesurfer? I am using my own average brain >>> that I created, but it would help to know how to do this for the fsaverage >>> as well. >>> >>> Many thanks for your help! >>> >>> >>> http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html >>> >>> >> > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 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] 3dClustSim and Gaussian filter width
Sorry for the repost of my last post, but I now realize that what I need is the estimated filter width that was actually used in the qdec analysis not the fwhm that I actually specified, i.e. 10 mm http://afni.nimh.nih.gov/afni/community/board/read.php?1,66182,66190#msg-66190 On Sun, Nov 29, 2015 at 2:51 PM, Emma Thompson <vonecono...@gmail.com> wrote: > Dear Freesurfers, > I am reposting my message in hopes that someone will reply this time > around - still grappling with this problem. Thanks. > > > > On Tue, Oct 27, 2015 at 8:59 AM, Emma Thompson <vonecono...@gmail.com> > wrote: > >> Dear Freesurfers, >> I am trying to use 3dclustsim in AFNI to determine the minimum number of >> voxel in a cluster to reach significance, my understanding is that in the >> command line the -fwhm s flag refers to the gaussian filter width and NOT >> the Gaussian Kernel, can anyone point me to how I might be able to obtain >> this for each hemisphere in freesurfer? I am using my own average brain >> that I created, but it would help to know how to do this for the fsaverage >> as well. >> >> Many thanks for your help! >> >> >> http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html >> >> > ___ 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] 3dClustSim and Gaussian filter width
Dear Freesurfers, I am reposting my message in hopes that someone will reply this time around - still grappling with this problem. Thanks. On Tue, Oct 27, 2015 at 8:59 AM, Emma Thompson <vonecono...@gmail.com> wrote: > Dear Freesurfers, > I am trying to use 3dclustsim in AFNI to determine the minimum number of > voxel in a cluster to reach significance, my understanding is that in the > command line the -fwhm s flag refers to the gaussian filter width and NOT > the Gaussian Kernel, can anyone point me to how I might be able to obtain > this for each hemisphere in freesurfer? I am using my own average brain > that I created, but it would help to know how to do this for the fsaverage > as well. > > Many thanks for your help! > > > http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html > > ___ 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] 3dClustSim and Gaussian filter width
Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be able to obtain this for each hemisphere in freesurfer? I am using my own average brain that I created, but it would help to know how to do this for the fsaverage as well. Many thanks for your help! http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html ___ 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] converting ROI .label to MNI space for SPM8
Thanks Douglas for your help! If I understand correctly, I will simply use
the aforementioned mri_label2vol script in my previous post but simply add
the option --regheader brainmask.mgz at the end?
On Mon, Aug 31, 2015 at 11:36 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> I'm not sure what is going wrong, but I would use mri_label2vol directly
> instead of using the combination of mri_convert and tkregister. Instead of
> passing it a registration file, use --regheader brainmask.mgz
>
>
> On 8/31/15 5:26 PM, Emma Thompson wrote:
>
> Forgive me, but I'm re-posting my query below hoping someone will respond
> this time around.
>
> Thanks in advance!
>
>
> Dear Freesurfers,
> I'm hoping you can help me resolve an issue I'm having with regard to
> converting my ROI labels from freesurfer space (Taliarach) to MNI space in
> prep for using these as seeds for a functional connectivity analysis.
>
> I created several ROIs labels (.label files), which I hand drew onto my
> study average brain (inflated surface) in qdec. I then used the following
> script to produce labels specific for each subject's brain in my analysis
>
> thePath='/pathtomydirectory/FS/subjects'
>
> subjects=(
> 'PAT01'\
> 'PAT02'\
> )
>
> nsubjects=${#subjects[*]}
> lastsubj=`expr $nsubjects - 1`
>
> for m in `seq 0 ${lastsubj}`
> do
>
> mri_label2label \
> --srcsubject MyAverageBrain \
> --srclabel ${thePath}/MyAverageBrain/label/lh.dACC.label \
> --trgsubject ${subjects[m]} \
> --trglabel ${thePath}/${subjects[m]}/label/lh.dACCi.label\
> --hemi lh \
> --regmethod surface
>
> done
>
>
> I then converted the .label files from .mgz format to nii using the
> following:
>
> mri_convert --in_type mgz --out_type nii --out_orientation RAS
> /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
> /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.nii.gz
>
> Next, I used the following scripts to get the registration matrix and to
> try and convert the label to a ROI that I can use in SPM:
>
> tkregister2 --mov /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
> --noedit --s PAT01 --regheader --reg
> /pathtomydirectory/FS/subjects/PAT01/mri/register.dat
>
> mri_label2vol --label
> /pathtomydirectory/FS/subjects/PAT01/label/lh.dACC.label --temp
> /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz --subject PAT01
> --hemi lh --o /pathtomydirectory/FS/subjects/PAT01_lhdACC.nii.gz --proj
> frac 0 1 .1 --fillthresh .3 --reg
> /pathtomydirectory/FS/subjects/PAT01/mri/register.dat
>
> the resulting ROI (PAT01_lhdACC.nii.gz) is close to the original surface
> ROI, but not exactly right, for example the ROI is a little more ventral
> than it should be when I overlay it onto mni152T1 average brain template.
>
> I'm not sure how to proceed or where I might have gone wrong, any ideas on
> how to go about this?
>
> Thanks!!!
>
> p.s. I love Freesurfer!!!
>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://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.
>
>
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] converting ROI .label to MNI space for SPM8
Forgive me, but I'm re-posting my query below hoping someone will
respond this time around.
Thanks in advance!
Dear Freesurfers,
I'm hoping you can help me resolve an issue I'm having with regard to
converting my ROI labels from freesurfer space (Taliarach) to MNI space in
prep for using these as seeds for a functional connectivity analysis.
I created several ROIs labels (.label files), which I hand drew onto my
study average brain (inflated surface) in qdec. I then used the following
script to produce labels specific for each subject's brain in my analysis
thePath='/pathtomydirectory/FS/subjects'
subjects=(
'PAT01'\
'PAT02'\
)
nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`
for m in `seq 0 ${lastsubj}`
do
mri_label2label \
--srcsubject MyAverageBrain \
--srclabel ${thePath}/MyAverageBrain/label/lh.dACC.label \
--trgsubject ${subjects[m]} \
--trglabel ${thePath}/${subjects[m]}/label/lh.dACCi.label\
--hemi lh \
--regmethod surface
done
I then converted the .label files from .mgz format to nii using the
following:
mri_convert --in_type mgz --out_type nii --out_orientation RAS
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.nii.gz
Next, I used the following scripts to get the registration matrix and to
try and convert the label to a ROI that I can use in SPM:
tkregister2 --mov /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
--noedit --s PAT01 --regheader --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat
mri_label2vol --label
/pathtomydirectory/FS/subjects/PAT01/label/lh.dACC.label --temp
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz --subject PAT01
--hemi lh --o /pathtomydirectory/FS/subjects/PAT01_lhdACC.nii.gz --proj
frac 0 1 .1 --fillthresh .3 --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat
the resulting ROI (PAT01_lhdACC.nii.gz) is close to the original surface
ROI, but not exactly right, for example the ROI is a little more ventral
than it should be when I overlay it onto mni152T1 average brain template.
I'm not sure how to proceed or where I might have gone wrong, any ideas on
how to go about this?
Thanks!!!
p.s. I love 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] converting ROI .labels to MNI space
Dear Freesurfers,
I'm hoping you can help me resolve an issue I'm having with regard to
converting my ROI labels from freesurfer space (Taliarach) to MNI space in
prep for using these as seeds for a functional connectivity analysis.
I created several ROIs labels (.label files), which I hand drew onto my
study average brain (inflated surface) in qdec. I then used the following
script to produce labels specific for each subject's brain in my analysis
thePath='/pathtomydirectory/FS/subjects'
subjects=(
'PAT01'\
'PAT02'\
)
nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`
for m in `seq 0 ${lastsubj}`
do
mri_label2label \
--srcsubject MyAverageBrain \
--srclabel ${thePath}/MyAverageBrain/label/lh.dACC.label \
--trgsubject ${subjects[m]} \
--trglabel ${thePath}/${subjects[m]}/label/lh.dACCi.label\
--hemi lh \
--regmethod surface
done
I then converted the .label files from .mgz format to nii using the
following:
mri_convert --in_type mgz --out_type nii --out_orientation RAS
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.nii.gz
Next, I used the following scripts to get the registration matrix and to
try and convert the label to a ROI that I can use in SPM:
tkregister2 --mov /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
--noedit --s PAT01 --regheader --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat
mri_label2vol --label
/pathtomydirectory/FS/subjects/PAT01/label/lh.dACC.label --temp
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz --subject PAT01
--hemi lh --o /pathtomydirectory/FS/subjects/PAT01_lhdACC.nii.gz --proj
frac 0 1 .1 --fillthresh .3 --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat
the resulting ROI (PAT01_lhdACC.nii.gz) is close to the original surface
ROI, but not exactly right, for example the ROI is a little more ventral
than it should be when I overlay it onto mni152T1 average brain template.
I'm not sure how to proceed or where I might have gone wrong, any ideas on
how to go about this?
Thanks!!!
p.s. I love 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.
Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory
Thanks Ani. Yes, I am simply trying to copy the cases to a new location (directory), so I can access and run my FS analyses from there. I had tried what you mentioned initially, following the wiki instructions for setup config, but I couldn't get it to source properly (I kept getting an error stating that -bash didn't recognize the setenv command). I started to think it just wasn't possible, really naive I know. I realize now after reading your post and perusing the listserve/internet for answers that this was because I was sourcing incorrectly in bash shell, so when I tried using the following 'export' command instead of 'setenv' everything works fine: export SUBJECTS_DIR=''/pathtomynewdirectory/subjects'' Thanks again!!! On Mon, Aug 10, 2015 at 3:09 PM, Ani Varjabedian a...@nmr.mgh.harvard.edu wrote: Hi Emma, You should be able to just copy the subject folders in question to a new location. When you want to work with them just set your SUBJECTS_DIR variable to whatever that new path is. Could you explain why you think you will have to recreate surface reconstructions? That should not be the case. You are simply going to copy the cases to a new location, correct? -Ani On 08/10/2015 02:49 PM, Emma Thompson wrote: Thanks Christopher for your response. I have read the tutorials/wiki page. My subject directory is set up somewhat similarly (See below). The problem is I would like to create and move the PP* patients to an entirely new and different FS 'subjects' directory while keeping the MM* patients in the current FS 'subjects' directory...Anybody have any ideas on how I can implement this? Thanks in advance! |-- STUDY A |-- DTI |-- FS |-- subjects |-- MM01 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- MM02 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- PP01 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- PP02 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash On Mon, Aug 10, 2015 at 2:26 PM, Watson, Christopher christopher.wat...@childrens.harvard.edu wrote: I think it's a bit unclear what you're asking for. Have you followed the tutorials on the wiki? Can you post your directory structure? What I do on my system is keep studies separate from one another. Each study directory has its own FS directory, and I keep the raw images separate. So something like the following: . |-- Study A |-- DTI |-- MPRAGE |-- raw |-- subj01 |-- subj01_mprage.nii.gz |-- subj01_DICOMS |-- subj02 |-- Freesurfer |-- subj01 |-- subj02 |-- FMRI ...and so on -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Emma Thompson [ vonecono...@gmail.com] *Sent:* Monday, August 10, 2015 2:16 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory Hi, I'm re-posting my query in case it got buried on the listserve: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my
Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory
Thanks Bruce for your response. I have only processed subjects in the 'old' directory that I am currently working in. I haven't overwritten anything or done anything in the new directory. Now that I am able to source this 'new' directory (pls see my previous post to Ani) correctly, my plan is to complete my processing in the old directory and then move everything over to the new directory and conduct my analyses there. I'm hoping this will circumvent having to redo anything (e.g., recon-all), does that sound correct to you? Thanks so much for your help! On Mon, Aug 10, 2015 at 3:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Emma can you clarify? Did you process one subject in a directory then overwrite it with a second? If so you probably can't recover it without rerunning recon-all. cheers Bruce On Mon, 10 Aug 2015, Emma Thompson wrote: Hi, I'm re-posting my query in case it got buried on the listserve: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! ___ 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 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] creating a new subject directory using imported data from existing subject directory
Hi, I'm re-posting my query in case it got buried on the listserve: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! ___ 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] creating a new subject directory using imported data from existing subject directory
Thanks Christopher for your response. I have read the tutorials/wiki page. My subject directory is set up somewhat similarly (See below). The problem is I would like to create and move the PP* patients to an entirely new and different FS 'subjects' directory while keeping the MM* patients in the current FS 'subjects' directory...Anybody have any ideas on how I can implement this? Thanks in advance! |-- STUDY A |-- DTI |-- FS |-- subjects |-- MM01 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- MM02 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- PP01 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash |-- PP02 |-- bem |-- label |-- mri |-- scripts |-- src |-- stats |-- surf |-- tmp |-- touch |-- trash On Mon, Aug 10, 2015 at 2:26 PM, Watson, Christopher christopher.wat...@childrens.harvard.edu wrote: I think it's a bit unclear what you're asking for. Have you followed the tutorials on the wiki? Can you post your directory structure? What I do on my system is keep studies separate from one another. Each study directory has its own FS directory, and I keep the raw images separate. So something like the following: . |-- Study A |-- DTI |-- MPRAGE |-- raw |-- subj01 |-- subj01_mprage.nii.gz |-- subj01_DICOMS |-- subj02 |-- Freesurfer |-- subj01 |-- subj02 |-- FMRI ...and so on -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Emma Thompson [ vonecono...@gmail.com] *Sent:* Monday, August 10, 2015 2:16 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory Hi, I'm re-posting my query in case it got buried on the listserve: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! ___ 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
Re: [Freesurfer] surface reconstruction and quality control
Thanks Michael for your comment, I'm wondering what others think in regard to your post. On Wed, Aug 5, 2015 at 5:44 PM, Harms, Michael mha...@wustl.edu wrote: Hi Emma, Martin, I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started excluding data of the sort that you showed, then there are going to be a lot of studies that would have to exclude a chunk of subjects. If that is the worst motion related artifact in your study, then you've been very successful at collecting good quality structurals! cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Emma Thompson vonecono...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, August 5, 2015 4:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surface reconstruction and quality control Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.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. -- The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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 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
[Freesurfer] creating a new subject directory using imported data from existing subject directory
Dear Freesurfers, I created a single subject directory and then imported sdata from two separate studies, in the end I realized I should have created two subject directories and would like to now rectify the situation. My question is, 1) how do I create a second subject directory in a different location? and 2) how do I transfer my existing subjects' data from my current subject directory to this new subject directory without having to redo any of my work (surface reconstruction). Is this even possible at this point? Or is it that I should only have one FS directory after all and perhaps I should just move the location of this directory so it is more accessible for both of my studies? If this is the case, could you advise me on how to go about doing this? BTW I'm using bash shell. I hope my questions are clear. Thanks!!! ___ 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] surface reconstruction and quality control
Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1016/j.neuroimage.2014.12.006 http://reuter.mit.edu/papers/reuter-motion14.pdf Best, Martin On 08/05/2015 02:55 PM, Emma Thompson wrote: Hi Freesurfers, I have a question regarding quality control. One of my subjects has pretty moderate ringing in their mprage image (presumably due to motion), I was thinking I should be excluding this subject, however I ran the subject through the pipeline anyway and I see that the segmentation and surfaces look ok. I'm wondering if based on this I should go ahead and include this subject for my analyses. I have attached a screenshot of the mprage and was hoping someone would take a look and give me their expert opinion. Thanks for you help! ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.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 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] LME analysis and fReadQdec.m
Dear Freesurfers,
I ran the following commands to read in mass-univariate data into matlab in
prep for LME analysis:
[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');
lhsphere = fs_read_surf('avgsubject/surf/lh.sphere');
lhcortex = fs_read_label('avgsubject/label/lh.cortex.label');
Next, I wanted to sort these data so that I could construct the design
matrix. Using instructions on the wiki, I ran the following command:
Qdec = fReadQdec('qdec.table.dat');
I received an error:
Error: File: fReadQdec.m Line: 5 Column: 1
Unexpected MATLAB operator.
Any ideas on what I'm doing wrong? I've attached an abbreviated version of
the qdec.table.dat file.
You're help is very much appreciated. Thanks!
long.qdec.table.dat
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Re: [Freesurfer] study specific template or fsaverage and LME analysis?
Thanks! On Mon, Dec 15, 2014 at 11:55 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is not possible to know whether this is a good idea or not. If you want to do it, here are the instructions doug # Create an average subject (Creates $SUBJECTS_DIR/newtemplate) make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... # Register each subject to the new template (do for both lh and rh) # Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate foreach subject (subj1 subj2 subj3 ...) cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere \ $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ surf/lh.sphere.reg.newtemplate end # Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... On 12/13/2014 02:03 PM, Emma Thompson wrote: Dear FS, I am getting ready to perform a LME analysis and am wondering if I should use my own study specific template or the fsaverage template provided by FS. I have a very small sample (n = 12). Also, I am looking across 4 different time points. I anticipate that I should create my own template, if so what are the procedures for doing this with the processed longitudinal data? Do I need to average each subjects brain across each time point, or is that redundant? Any clarification on how to go about this would be greatly appreciated. Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] study specific template or fsaverage and LME analysis?
Dear FS, I am getting ready to perform a LME analysis and am wondering if I should use my own study specific template or the fsaverage template provided by FS. I have a very small sample (n = 12). Also, I am looking across 4 different time points. I anticipate that I should create my own template, if so what are the procedures for doing this with the processed longitudinal data? Do I need to average each subjects brain across each time point, or is that redundant? Any clarification on how to go about this would be greatly appreciated. Thanks! ___ 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] cortical surface area measurement and vertex-wise analysis
Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Thanks for your help and apologizes for my silly questions. On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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 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 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] cortical surface area measurement and vertex-wise analysis
Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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] longitudinal analysis and linear mixed effects models
Hi FS, I want to conduct a within-subjects longitudinal analysis, I thought I would be able to run a LME model in QDEC but this doesn't seem to be the case at all, is this correct? It seems I have to do everything using Matlab (big sigh). https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels I have already preprocessed the data: 1) cross for all time points, 2) base, and then 3) long according to the awesome tutorial provided by FS. I have only one group, a patient population that was scanned prior to (bseline) and at various time points (3 time points post) following treatment. Would you agree that the best analytical approach for me would be the LME model, especially since I have a few subjects with a couple of missing post-treatment time points? Is there any way you would recommend another approach using QDEC? Lastly, I have done everything in FS version 5.1, I'm considering upgrading to 5.3, since my freeview software seems to be out of date. It also seems that the Matlab tools I need to run LME are only available in FS version 5.2. At this point a little concerned since I'm hoping I didn't waste a bunch of time just realizing all this now, would upgrading to 5.3 negatively impact all the work I've done thus far using version 5.1? Thanks for the help!! ___ 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] missing time point and longitudinal analysis
Hi Freesurfers, I'm conducting a longitudinal analysis but have several subjects with a few missing time points. The paradigm contained 4 time points in total, a baseline that occurred prior to any treatment and 3 post-treatment time points. All my subjects have baseline time points. However, a few subjects have a missing post-treatment time point. Can I still use these subjects in my longitudinal analysis even though 1 of the 3 post-treatment time points are missing? Thanks in advance for your help! ___ 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] missing time point and longitudinal analysis
Thanks so much Martin! On Mon, Sep 22, 2014 at 9:51 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Emma, yes, you can use these subjects. In fact for linear mixed effects models it makes even sense to include subjects that have only a single time point (if that is the small minority of course). Simply follow the same steps: cross for all time points, base (even if you include only a single time point here) and then long. Best, Martin On 09/22/2014 09:35 AM, Emma Thompson wrote: Hi Freesurfers, I'm conducting a longitudinal analysis but have several subjects with a few missing time points. The paradigm contained 4 time points in total, a baseline that occurred prior to any treatment and 3 post-treatment time points. All my subjects have baseline time points. However, a few subjects have a missing post-treatment time point. Can I still use these subjects in my longitudinal analysis even though 1 of the 3 post-treatment time points are missing? Thanks in advance for your help! ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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 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] interpreting qdec results
That would be especially helpful, thanks Doug. I have another related question. In addition to measuring cortical thickness, I've also done the same analysis using the cortical surface volume measure in Qdec. For this analysis I used age and mean centered total intercranial volume (TIV) as nuisance variables. After running the analysis, the graph is displayed showing the volume on the y axis and mean centered TIV on the y axis. When I extract the data I get volume values in the 2.0016 - 2.7268 range, I was expecting to see values on the order of 1500-1600 or so, is this because qdec is giving me cortical volume values that have been normalized to TIV? Thanks again for all your help! On Wed, Jun 25, 2014 at 5:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: No, I've never used SPSS. If you know matlab, I can step you through how to do it there On 06/25/2014 04:13 PM, Emma Thompson wrote: I'm using SPSS. I'm not sure if my analysis reflects exactly what qdec is doing, do you know which analysis in SPSS would be most appropriate? I'm doing a simple ANCOVA. On Wed, Jun 25, 2014 at 11:07 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: what software did you use? Are you sure you are using the same model as qdec uses? On 06/25/2014 11:03 AM, Emma Thompson wrote: Thanks Doug, yes I did control for age in both instances. On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Your interpretation is right (ie, controls patients for red/yellow/orange). When you compared the two groups in your separate analysis, did you control for age? doug On 06/24/2014 02:19 PM, Emma Thompson wrote: Hi Freesurfers, I am reposting this as my last email bounced. I have conducted a DODS analysis in qdec with group (controls vs patients) set as my fixed factor and age as a nuisance variable to determine if my groups differ in cortical thickness. Controls were added first in the .levels file followed by patients. When I view the results in the display window for do controls differ from patients in cortical thickness I see a significant cluster for the caudal anterior cingulate, denoted by a red-orange blob and a positive t-value. I'm wondering if this simply means that controls had greater cortical thickness compared to patients after controlling for age? The reason I ask is that I'm a little confused since when I created an ROI for this cluster using tksurfer and then extracted the means and sd, I see that the patients actually have larger means than the controls, the opposite of my interpretation of the results presented by the qdec display. Furthermore, if I extract the means and sds for the entire caudal anterior cingulate using the aparc file, I get means that are larger in controls, compared to patients, which seems consistent with qdec. Any ideas? Thanks for all the help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer
Re: [Freesurfer] interpreting qdec results
Thanks Doug, yes I did control for age in both instances. On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Your interpretation is right (ie, controls patients for red/yellow/orange). When you compared the two groups in your separate analysis, did you control for age? doug On 06/24/2014 02:19 PM, Emma Thompson wrote: Hi Freesurfers, I am reposting this as my last email bounced. I have conducted a DODS analysis in qdec with group (controls vs patients) set as my fixed factor and age as a nuisance variable to determine if my groups differ in cortical thickness. Controls were added first in the .levels file followed by patients. When I view the results in the display window for do controls differ from patients in cortical thickness I see a significant cluster for the caudal anterior cingulate, denoted by a red-orange blob and a positive t-value. I'm wondering if this simply means that controls had greater cortical thickness compared to patients after controlling for age? The reason I ask is that I'm a little confused since when I created an ROI for this cluster using tksurfer and then extracted the means and sd, I see that the patients actually have larger means than the controls, the opposite of my interpretation of the results presented by the qdec display. Furthermore, if I extract the means and sds for the entire caudal anterior cingulate using the aparc file, I get means that are larger in controls, compared to patients, which seems consistent with qdec. Any ideas? Thanks for all the help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] interpreting qdec results
I'm using SPSS. I'm not sure if my analysis reflects exactly what qdec is doing, do you know which analysis in SPSS would be most appropriate? I'm doing a simple ANCOVA. On Wed, Jun 25, 2014 at 11:07 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what software did you use? Are you sure you are using the same model as qdec uses? On 06/25/2014 11:03 AM, Emma Thompson wrote: Thanks Doug, yes I did control for age in both instances. On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Your interpretation is right (ie, controls patients for red/yellow/orange). When you compared the two groups in your separate analysis, did you control for age? doug On 06/24/2014 02:19 PM, Emma Thompson wrote: Hi Freesurfers, I am reposting this as my last email bounced. I have conducted a DODS analysis in qdec with group (controls vs patients) set as my fixed factor and age as a nuisance variable to determine if my groups differ in cortical thickness. Controls were added first in the .levels file followed by patients. When I view the results in the display window for do controls differ from patients in cortical thickness I see a significant cluster for the caudal anterior cingulate, denoted by a red-orange blob and a positive t-value. I'm wondering if this simply means that controls had greater cortical thickness compared to patients after controlling for age? The reason I ask is that I'm a little confused since when I created an ROI for this cluster using tksurfer and then extracted the means and sd, I see that the patients actually have larger means than the controls, the opposite of my interpretation of the results presented by the qdec display. Furthermore, if I extract the means and sds for the entire caudal anterior cingulate using the aparc file, I get means that are larger in controls, compared to patients, which seems consistent with qdec. Any ideas? Thanks for all the help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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
[Freesurfer] interpreting qdec results
Hi Freesurfers, I am reposting this as my last email bounced. I have conducted a DODS analysis in qdec with group (controls vs patients) set as my fixed factor and age as a nuisance variable to determine if my groups differ in cortical thickness. Controls were added first in the .levels file followed by patients. When I view the results in the display window for do controls differ from patients in cortical thickness I see a significant cluster for the caudal anterior cingulate, denoted by a red-orange blob and a positive t-value. I'm wondering if this simply means that controls had greater cortical thickness compared to patients after controlling for age? The reason I ask is that I'm a little confused since when I created an ROI for this cluster using tksurfer and then extracted the means and sd, I see that the patients actually have larger means than the controls, the opposite of my interpretation of the results presented by the qdec display. Furthermore, if I extract the means and sds for the entire caudal anterior cingulate using the aparc file, I get means that are larger in controls, compared to patients, which seems consistent with qdec. Any ideas? Thanks for all the help. ___ 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.
