Re: [Freesurfer] convert FSFAST files to gifti format
Doug- I did try mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz fmcpr.lh.gifit-file.gii I still get freadFloat: frear failed error. On separate note: Is is possible to convert these FSFAST generated files (fmcpr.odd.sm5.fsaverage.?h.nii.gz and fmcpr.odd.sm5.mni305.2mm.nii.gz) into CIFTI format? -Sabin On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka wrote: > Hi Doug- I did try > mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white > $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz > fmcpr.lh.gifit-file.gii > > I still get freadFloat: frear failed error. > > Cheers, > Sabin Khadka > > On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> what is your mris_convert command line? You need to include vertex >> position information (eg, -o lh.white) >> >> >> On 09/12/2016 03:32 PM, Sabin Khadka wrote: >> > Hi all, >> > >> > Is there a way to convert FSFAST files >> > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti >> > format? I've tried mris_convert but it does not work. >> > >> > Thanks for help. >> > >> > Cheers, >> > Sabin Khadka >> > >> > >> > ___ >> > 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] convert FSFAST files to gifti format
Hi Doug- I did try mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz fmcpr.lh.gifit-file.gii I still get freadFloat: frear failed error. Cheers, Sabin Khadka On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve wrote: > what is your mris_convert command line? You need to include vertex > position information (eg, -o lh.white) > > > On 09/12/2016 03:32 PM, Sabin Khadka wrote: > > Hi all, > > > > Is there a way to convert FSFAST files > > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti > > format? I've tried mris_convert but it does not work. > > > > Thanks for help. > > > > Cheers, > > Sabin Khadka > > > > > > ___ > > 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] convert FSFAST files to gifti format
Hi all, Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti format? I've tried mris_convert but it does not work. Thanks for help. Cheers, Sabin Khadka ___ 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] FSFAST ROI atlas
Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael wrote: > > They are attached (assuming that the FS list allows small attachments). > There is a script that details exactly how it was done. > > -- > 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: Sabin Khadka > Date: Wednesday, August 17, 2016 at 11:25 AM > To: Freesurfer support list , "Harms, > Michael" > > Subject: Re: [Freesurfer] FSFAST ROI atlas > > Hi Michael- Is there anyway I can get those Gordon parcellation annot > files? > > Cheers, > Sabin Khadka > > On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael wrote: > >> >> FYI: I supplied a version of the “Gordon” parcellation in .annot format >> to Bruce a while back. He had expressed an interest in possibly including >> it as part of FS 6.0. >> >> 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: on behalf of Doug Greve < >> gr...@nmr.mgh.harvard.edu> >> Reply-To: "freesurfer@nmr.mgh.harvard.edu" > u> >> Date: Wednesday, August 17, 2016 at 9:55 AM >> To: "freesurfer@nmr.mgh.harvard.edu" >> Subject: Re: [Freesurfer] FSFAST ROI atlas >> >> I don't know anything about the Power atlas. For the HCP, if they have it >> in annotation format, then you can run mri_aparc2aseg to map it into the >> anatomical volume, then specify that volume when you run fcseed-config. To >> get the mri_aparc2aseg command line, look in the recon-all to find out how >> aparc+aseg.mgz is created >> >> On 8/17/16 9:28 AM, Sabin Khadka wrote: >> >> Hi Doug- Do you think it is possible to use these atlas? If so could you >> point me to steps that needed to be done. >> >> Thanks for your help! >> >> Cheers, >> Sabin Khadka >> >> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> I have not used them myself. >>> >>> On 8/15/16 10:23 AM, Sabin Khadka wrote: >>> >>> HI all- >>> >>> I am using FSFAST to extract ROI time series values for further >>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas. >>> >>> However, I was wondering if anyone has used Power et.al 2011 rois >>> and/or HCP's newly defined 180/per hemi rois to extract time series data. >>> If so could you please advise me on how do it (if they are at all >>> possible). >>> >>> Cheers, >>> Sabin Khadka >>> >>> >>> ___ >>> 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.e >>> du/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 >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> >> 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
Re: [Freesurfer] FSFAST ROI atlas
Hi Michael- Is there anyway I can get those Gordon parcellation annot files? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael wrote: > > FYI: I supplied a version of the “Gordon” parcellation in .annot format to > Bruce a while back. He had expressed an interest in possibly including it > as part of FS 6.0. > > 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: on behalf of Doug Greve < > gr...@nmr.mgh.harvard.edu> > Reply-To: "freesurfer@nmr.mgh.harvard.edu" > > Date: Wednesday, August 17, 2016 at 9:55 AM > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] FSFAST ROI atlas > > I don't know anything about the Power atlas. For the HCP, if they have it > in annotation format, then you can run mri_aparc2aseg to map it into the > anatomical volume, then specify that volume when you run fcseed-config. To > get the mri_aparc2aseg command line, look in the recon-all to find out how > aparc+aseg.mgz is created > > On 8/17/16 9:28 AM, Sabin Khadka wrote: > > Hi Doug- Do you think it is possible to use these atlas? If so could you > point me to steps that needed to be done. > > Thanks for your help! > > Cheers, > Sabin Khadka > > On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve > wrote: > >> I have not used them myself. >> >> On 8/15/16 10:23 AM, Sabin Khadka wrote: >> >> HI all- >> >> I am using FSFAST to extract ROI time series values for further >> connectivity analysis. I've used Desikan, Destriuex and DKT atlas. >> >> However, I was wondering if anyone has used Power et.al 2011 rois and/or >> HCP's newly defined 180/per hemi rois to extract time series data. If so >> could you please advise me on how do it (if they are at all possible). >> >> Cheers, >> Sabin Khadka >> >> >> ___ >> 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.e >> du/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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > > 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 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] FSFAST ROI atlas
Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done. Thanks for your help! Cheers, Sabin Khadka On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve wrote: > I have not used them myself. > > On 8/15/16 10:23 AM, Sabin Khadka wrote: > > HI all- > > I am using FSFAST to extract ROI time series values for further > connectivity analysis. I've used Desikan, Destriuex and DKT atlas. > > However, I was wondering if anyone has used Power et.al 2011 rois and/or > HCP's newly defined 180/per hemi rois to extract time series data. If so > could you please advise me on how do it (if they are at all possible). > > Cheers, > Sabin Khadka > > > ___ > 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.
[Freesurfer] FSFAST ROI atlas
HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). Cheers, Sabin Khadka ___ 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] MNI coordinates of all the vertices of fsaverage
Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka wrote: > Hi Doug, I tried to pick up from the thread below to get MNI coordinates > of each destrieux parcellation region. > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html > > I created label files from > mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation > aparc.a2009s --outdir label_destrieux # which works fine > > And I tried to get the coordinates of each labels using > > mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel > --sum --centroid --thmin 0 > --hemi lh --subject fsaverage > > But, all left labels would produce the same coordinates and so does right > labels. (I've attached few example files here with). Also, it says TalX, > TalY, TalZ are these coordinates in MNI or Talairach? > > Thanks for 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] MNI coordinates of all the vertices of fsaverage
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel --sum --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help. rh_G_S_Ant Description: Binary data rh_S_suborbital Description: Binary data lh_S_suborbital Description: Binary data lh_G_S_Ant Description: Binary data ___ 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] FSFAST time series extraction
Hi Doug,
Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from
Buckner 2011 7 Cerebellar network. Please see below for the steps I
performed to extract time series from Buckner 2011 7 Cerebellar networks.
If you could give your thoughts on the steps/process that'd be great.
*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all Yeo2011_MNI152_FS
*2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to
freesurfe nonlinear volumetric space*
mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
*3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear*
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
*4. Create a cerebellum gray matter mask in the native subject's space by
applying mri_binarize to aparc2009s+aseg.mgz of the subject*
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --o
cerebellum_mask_FSSub_m8.nii.gz # For left
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o
cerebellum_mask_FSSub_m47.nii.gz # FOr right
*5. Using this mask to mask the Buckner cerebellum parcellations*
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8.nii.gz # For
left
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47.nii.gz # For
right
*6. Functional data to anatomical space*
mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz # functional into anatomical space
*7. Extract L/R Cerebellar ROIs time series*
mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m8.nii.gz --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt #
extract Left Cerebellum time series
mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m47.nii.gz --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt #
extract right Cerebellum time series
Cheers,
Sabin Khadka
On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve
wrote:
> has this question been answered?
>
> On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> > Hi all,
> >
> > I am trying to extract mean time series BOLD data using FSFAST from
> > Cortical ROIs + sub cortical ROIs and cerebellum.
> >
> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> > -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc
> > --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid
> > 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> > mri_segstats --annot fsaverage rh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >
> > and for cortical time series
> >
> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> > --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id
> > 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz
> > --avgwf subCorticalTimeSeries.txt
> >
> > But I am not sure on how exactly to extract time series from
> > cerebellar regions. So if I want to extract time series from regions
> > as described in Buckner et.al 2011. Could I just use mri_segstats for
> > the labels 601-628 in FreeSurferCololLUT.txt? If not could you please
> > direct me to processes that I can use.
> >
> >
> >
> > Sent from Yahoo Mail. Get the ap <https://yho.com/148vdq>
> >
> >
> > ___
> > 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/
>
>
Re: [Freesurfer] FSFAST- Cerebellum
Hi Thomas- On second thought is it valid to simply do if I want average time series of the cerebellum regions? fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> avgCerebellum.txt Is this correct? Cheers, Sabin Khadka On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka wrote: > Hi Thomas and Doug- > > Thanks for you suggestions. Per your suggestions I performed following > > recon-all -i > $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz > -subjid Yeo2011_MNI152_FS > > recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS > > mri_vol2vol --mov > $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz > \ > --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z > talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest > > mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ > BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o > Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph > > mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o > cerebellum_mask_FSSub.nii.gz > > fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz > Buckner_atlas_FSSub > > mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o > fmcpr.anat.nii.gz > > mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf > test.txt > > However, I got the following error > ERROR: must specify a segmentation volume > > Am I doing anything wrong here. Do you have any suggestions/fixes? > > > Cheers, > Sabin Khadka > > On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo wrote: > >> Hi Doug, thanks. >> >> Hi Sabin, you can use the following steps to transform the Buckner >> cerebellum atlas to your subject's native anatomical space and then >> follow Doug's instructions (taken and adapted from another user >> Bronwyn's email): >> >> 1. Run MNI152 1mm template through recon-all >> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid >> Yeo2011_MNI152_FS >> >> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer >> nonlinear volumetric space >> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ >> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o >> BucknerAtlas1mm_FSI.nii.gz --nearest >> >> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear >> volumetric space to each subject: >> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ >> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o >> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph >> >> 4. Create a cerebellum gray matter mask in the native subject's space >> by applying mri_binarize to aparc+aseg.mgz of the subject >> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o >> cerebellum_mask_subjID.nii.gz >> >> 5. Using this mask to mask the Buckner cerebellum parcellations >> fslmaths Buckner2011_atlas_subjID.nii.gz -mas >> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz >> >> Regards, >> Thomas >> >> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve >> wrote: >> > yes >> > >> > >> > >> > On 6/24/16 9:19 AM, Thomas Yeo wrote: >> >> >> >> Hi Doug, >> >> >> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin >> >> passed in the cerbellum parcellation in the same anatomical space as >> >> aseg? >> >> >> >> --Thomas >> >> >> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve >> >> wrote: >> >>> >> >>> After you run preproc-sess, there will be a file called >> >>> register.dof6.dat. >> >>> Map fmri into the anatomical space, something like >> >>> >> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o >> >>> fmcpr.anat.nii.gz >> >>> >> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz >> >>> >> >>> However, I don't think that the aseg has those cerebellum >> parcellations. >> >>> >> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote: >> >>> >> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 >> >>> space. I >> >>> process my fmri data with >> >>> >> >&g
Re: [Freesurfer] FSFAST- Cerebellum
Hi Thomas and Doug- Thanks for you suggestions. Per your suggestions I performed following recon-all -i $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz -subjid Yeo2011_MNI152_FS recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS mri_vol2vol --mov $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o cerebellum_mask_FSSub.nii.gz fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz Buckner_atlas_FSSub mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o fmcpr.anat.nii.gz mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf test.txt However, I got the following error ERROR: must specify a segmentation volume Am I doing anything wrong here. Do you have any suggestions/fixes? Cheers, Sabin Khadka On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo wrote: > Hi Doug, thanks. > > Hi Sabin, you can use the following steps to transform the Buckner > cerebellum atlas to your subject's native anatomical space and then > follow Doug's instructions (taken and adapted from another user > Bronwyn's email): > > 1. Run MNI152 1mm template through recon-all > recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid > Yeo2011_MNI152_FS > > 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer > nonlinear volumetric space > mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ > $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o > BucknerAtlas1mm_FSI.nii.gz --nearest > > 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear > volumetric space to each subject: > mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ > BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o > Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph > > 4. Create a cerebellum gray matter mask in the native subject's space > by applying mri_binarize to aparc+aseg.mgz of the subject > mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o > cerebellum_mask_subjID.nii.gz > > 5. Using this mask to mask the Buckner cerebellum parcellations > fslmaths Buckner2011_atlas_subjID.nii.gz -mas > cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz > > Regards, > Thomas > > On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve > wrote: > > yes > > > > > > > > On 6/24/16 9:19 AM, Thomas Yeo wrote: > >> > >> Hi Doug, > >> > >> Would your mri_segstats command work if instead of aseg.mgz, Sabin > >> passed in the cerbellum parcellation in the same anatomical space as > >> aseg? > >> > >> --Thomas > >> > >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve > >> wrote: > >>> > >>> After you run preproc-sess, there will be a file called > >>> register.dof6.dat. > >>> Map fmri into the anatomical space, something like > >>> > >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o > >>> fmcpr.anat.nii.gz > >>> > >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz > >>> > >>> However, I don't think that the aseg has those cerebellum > parcellations. > >>> > >>> On 6/21/16 5:52 PM, Sabin Khadka wrote: > >>> > >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 > >>> space. I > >>> process my fmri data with > >>> > >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 > -fwhm 6 > >>> -per-run -stc odd > >>> and then to extract ROI time series values I did > >>> > >>> mri_segstats --annot fsaverage rh aparc --i > >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 > >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt > >>> > >>> and for cortical time series > >>> > >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab > >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 > >>> --id > >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id > >>
Re: [Freesurfer] FSFAST- Cerebellum
Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I process my fmri data with preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd and then to extract ROI time series values I did mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt Now I am not sure as how to extract cerebellum ROIs (time series as described in Buckner et.al 2011)? If there are any other additional steps I need to perform ? or if I have to use some other scripts commands (other than mri_segstats). Cheers, Sabin Khadka On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo wrote: > Hi Sabin, > > The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical > substructures of the cerebellum (e.g., Crus I, etc). Is that what you > want? Or are you looking to use the functional parcels defined in > Buckner 2011? > > In addition, I do not know how mri_segstats works, so I cannot verify > how you call the command is correct. Maybe others can provide feedback > here. > > However, the Buckner cerebellar parcellations in > $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152 > space. From your command, I assume your data is in MNI305 space. So > you might need to transform the parcellation from MNI152 to MNI305. > > Thanks, > Thomas > > On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka > wrote: > > Hi all, > > > > I am trying to extract mean time series BOLD data using FSFAST from > Cortical > > ROIs + sub cortical ROIs and cerebellum. > > > > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 > > -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i > > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 > > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt > > mri_segstats --annot fsaverage rh aparc --i > > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 > > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt > > > > and for cortical time series > > > > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab > > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 > --id > > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id > 58 > > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf > > subCorticalTimeSeries.txt > > > > But I am not sure on how exactly to extract time series from cerebellar > > regions. So if I want to extract time series from regions as described in > > Buckner et.al 2011. Could I just use mri_segstats for the labels > 601-628 in > > FreeSurferCololLUT.txt? If not could you please direct me to processes > that > > I can use. > > > > Cheers, > > Sabin Khadka > > > > ___ > > 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 > ___ 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] FSFAST- Cerebellum
Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka ___ 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] FSFAST- Cerebellum
Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka___ 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] Significant clusters from mri_glmfit
Hi all, I used FDR correction method to correct for multiple comparison after mri_glmfit. And I have a cluster covering multiple regions. I want to extract the thickness, surface area, lgi values for local maxima (or, multiple regions covered by the big significant cluster). I see it is not straightforward as when monte-carlo cluster correction is applied. Can anyone suggest me if there is a work around for this apart from manually creating a ROI masks and extracting values? Thanks for help! Cheers, Sabin Khadka___ 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 question
Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? 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] Qdec questions
Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? 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] Qdec - cluster labels
Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks,Sabin ___ 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] FSFAST
Hi all,If I understand correctly, preproc-sess command takes mid point of EPI image as reference and make template and calculate motion parameters. I could not figure if I could use different image as reference, is it possible? Cheers, Sabin Khadka___ 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] FS-FAST bbr registration
Hi all- Is there a command we can have screenshots (similar to one employed in fsl) of fucntional--> structural registration in FSFAST to visually check the registration on top of the BBR cost? Cheers, Sabin Khadka ___ 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] FSFAST
Hi FS Users- After using FSFAST's preproc-sess command (I get the output files: fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well the EPIs are mapping onto the common space (I am assuming fsaverage in this case)?Also, is there a way to band pass filter these time series data. I want to use band pass filter and then use the mean time series of FS parcellation regions and analyze the data outside the FSFAST console. Cheers, Sabin Khadka___ 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] time series data from FSFAST
Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum Cheers, Sabin Khadka From: Douglas Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 3:32 PM Subject: Re: [Freesurfer] time series data from FSFAST On 2/9/15 3:16 PM, sabin khadka wrote: Thanks Doug. I am now able to get average time series from cortical ROIs. I used mri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt That's right, but I would use the unsmoothed data since smoothing will cause activity to spill-over between regions. How would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)? I tried doing mri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt but it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Use fsaverage/mri.2mm/aseg.mgz doug Cheers, Sabin Khadka From: Douglas Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ 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 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 ___ 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] time series data from FSFAST
Thanks Doug. I am now able to get average time series from cortical ROIs. I usedmri_segstats --annot fsaverage lh aparc --i sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txtHow would I get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)?I tried doingmri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txtbut it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions. Cheers, Sabin Khadka From: Douglas Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 9, 2015 1:24 PM Subject: Re: [Freesurfer] time series data from FSFAST Yes, mri_segstats. Run it with --help. See esp example 6 On 2/9/15 12:31 PM, sabin khadka wrote: Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka ___ 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 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] time series data from FSFAST
Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the command to get the time-series of all the ROIs at once in a .txt or .dat files but I am not sure how exactly to do it. Thanks for help. Cheers, Sabin Khadka___ 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] Extract mean time series from parcellated region
Works fine. thanks for the help Doug. Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer support list Sent: Tuesday, January 27, 2015 12:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region That label2vol command maps the aseg into the epi space to create test1 so it will only have 1 frame. The epi never comes into play there except as a geometry template. If you want to extract a time course from the epi, then map it to the anatomical space with that vol2vol command using the epi as the --mov, then run mri_segstats. That label2vol command is not necessary. doug On 1/27/15 12:13 PM, sabin khadka wrote: Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run # mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gz EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer support list Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer Support List Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gz # mri_segstats --seg --id --in test2.nii.gz --avgwf I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 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.pa
Re: [Freesurfer] Extract mean time series from parcellated region
Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run# mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz# mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gzEPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer support list Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer Support List Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gz # mri_segstats --seg --id --in test2.nii.gz --avgwf I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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.
Re: [Freesurfer] Extract mean time series from parcellated region
Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer Support List Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gz # mri_segstats --seg --id --in test2.nii.gz --avgwf I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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] Extract mean time series from parcellated region
Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold# mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ --reg register.dat --o test2.nii.gz# mri_segstats --seg --id --in test2.nii.gz --avgwf I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka___ 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] Parcellated regions as masks?
Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI? Cheers, Sabin Khadka From: Douglas N Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 21, 2015 1:59 PM Subject: Re: [Freesurfer] Parcellated regions as masks? establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: > Hi FS users, > > We've T1 and EPI images collected. For my analysis I want to use FS > parcellated regions (both cortical/sub-cortical regions) as ROIs > (Masks) for my functional images. Would anyone kindly let me know what > is the best way to proceed. > Cheers, > Sabin Khadka > > > ___ > 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] Parcellated regions as masks?
Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka___ 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] extract mean thickness, surface area of ROI
Hi all, I want to extract mean cortical thickness, surface area of an ROI I created with some clusters that showed some group difference. I already have the ROIs I need. What is the easiest way to extract mean values of ROI from all the subjects? Thanks, Sabin___ 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] 2x3 ANOVA question
Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DOSS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2HighClass FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin ___ 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] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi all, I ran mri_surf2surf and then mris_convert to get vertexwise thickness and surface area values in ascii files. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:30 AM, sabin khadka wrote: Ahh. Great. Thanks you very much for the information. I ran mri_surf2surf and then mris_convert to get thickness and surface area vertex wise values. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:10 AM, Bruce Fischl wrote: yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: > Hi Bruce, > Thanks for the reply. I was wondering if I have to somehow resample or map > to fsaverage so as to have same # of vertices across all subjects. I tried > using mris_convert as you suggested above but I can see that different > subjects have different #of vertices. > > Thanks for help. > > -Sabin > On Thursday, April 17, 2014 9:29 AM, Bruce Fischl > wrote: > Hi Sabin > > mris_convert can convert binary "curvature" format files to ascii ones if > the output file has the extension asc. Something like: > > mris_convert -c lh.thickness lh.orig lh.thickness.asc > > this will give you a 5 column ascii file in the format > > > cheers > Bruce > > On Thu, 17 Apr 2014, > sabin khadka > wrote: > > > Hi all, > > I want to extract to extract thickness, area and lgi values vertex wise in > > ascii files for group of subjects. Could anyone suggest me on how to do > it. > > > > Thank you for your help. > > > > -Sabin > > > > > > > > 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] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin On Thursday, April 17, 2014 9:29 AM, Bruce Fischl wrote: Hi Sabin mris_convert can convert binary "curvature" format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: > Hi all, > I want to extract to extract thickness, area and lgi values vertex wise in > ascii files for group of subjects. Could anyone suggest me on how to do it. > > Thank you for your help. > > -Sabin > > 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] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?
Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin___ 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] Thickness values to a common space
Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv Step 2: mris_convert -c SUB001-area ?h.white SUB001-area.asc Can you direct me on how to get vertex wise thickness, surface area and pial_lgi values for a subject and extract in a ascii file. And also, if I want to convert ascii file with thickness values to freesurfer format, how would I do it? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: > Hi all, > > Related question to this. > I am trying to extract vertexwise surface area values in an ascii > files. For that I am doing > > mri_surf2surf --hemi ?h --srcsubject area --src_type > curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv > mris_convert -c XYZ-area ?h.white XYZ-area.asc > > However I am getting surface area values for some vertices as negative. > 1) Am I following correct steps while writing vertex-wise values in > ascii files? > 2) Aren't values of surface-area supposed to be non-negative? > > I am not sure what I am missing here. For some reason I am not able to > post questions to freesurfer support list by myself. > > Thanks for the help. > > -Sabin > > On Friday, April 11, 2014 3:18 PM, Jonathan Holt > wrote: > I’m trying to find a way to extract thickness values at each vertex > for a given subject, and as a part of that process I need to ensure > that each subject has been mapped to a common area, such that their > vertices have a direct correspondence, but I’m not entirely sure how > to go about it. > > I’ve started with mris_preproc but the output is an mgh, which I’m not > sure is useful for my endeavor. > ___ > 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 not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Thickness values to a common space
Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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] vertex wise surface area measure?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin ___ 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] vertex-wise surface area values?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin ___ 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] test- please disregard
Sorry all. Just a test 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] test- please disregard
- ___ 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] vertex wise surface area values?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin ___ 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] Vertex wise surface area values?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin Sent from my iPhone ___ 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] Vertexwise surface area value?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin___ 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] asegstats2table error
All aseg.stats seems to have volume of 45 ROIs with some hypointensities value =0. Also, I checked aseg.mgz and looks fine with these subjects. I extracted values with asegstats2table with --all-seg flag. I hope that is okay? On Sunday, March 2, 2014 11:28 AM, Douglas Greve wrote: That means that it was expecting to find 66 segmentations but only found 55. Sometimes there are some segmentations in one subject that are not in another (usually hypointensities). But 11 is too many. Have you looked at the aseg to see if it looks right? You can also compare the aseg.stats file to see which segs are missing. doug On 3/2/14 9:46 AM, sabin khadka wrote: Hi all, >While using asegstats2table, I got following error for few subjects, >WARN SUBID: nmeasure 66, expecting 55 >It let me extract cortical thickness and surface area using aparcstats2table >though. >Any suggestions? > > >-SABIN > > >___ 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 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] asegstats2table error
Hi all, While using asegstats2table, I got following error for few subjects, WARN SUBID: nmeasure 66, expecting 55 It let me extract cortical thickness and surface area using aparcstats2table though. Any suggestions? -SABIN___ 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] No labels file in label directory?
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this. -Sabin___ 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] fReadQdec question
Its under freesurfer/matlab/lme/Qdec. This is what is suggested to use while performing linear mixed effects models in freesurfer. http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels On Tuesday, February 18, 2014 3:35 PM, Douglas N Greve wrote: where did you get this m file from? I don't see it in our distribution. On 02/18/2014 03:29 PM, sabin khadka wrote: > Hi Doug, > Thanks for the reply. Yeah I have my qdec.table.dat file in the same > format as wiki says and in tab delimited format. But when I try to run > fReadQdec it reads it as N(# of subjects)X1 cell (discounting for all > tabs and spaces). I was assuming it would give me N X M(no of columns > for each variable that I put in table). > > -Sabin > > > On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve > wrote: > > yes, it has a certain format. Look at the examples on the wiki > doug > > On 02/18/2014 11:19 AM, sabin khadka wrote: > > Hi all, > > I am trying to run fReadQdec.m. My qdec.table.dat file is a tab > > delimited file. However when it reads to Qdec variable it reads it as > > N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried > > debugging the code but it seems to me like it is just a simple read > > file in matlab. Does the qdec.table.dat file need to be in certain > format? > > > > -Sabin > > > > > > > > > ___ > > 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 > 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 <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. > > > > -- 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 not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] fReadQdec question
Hi Doug, Thanks for the reply. Yeah I have my qdec.table.dat file in the same format as wiki says and in tab delimited format. But when I try to run fReadQdec it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I was assuming it would give me N X M(no of columns for each variable that I put in table). -Sabin On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve wrote: yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: > Hi all, > I am trying to run fReadQdec.m. My qdec.table.dat file is a tab > delimited file. However when it reads to Qdec variable it reads it as > N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried > debugging the code but it seems to me like it is just a simple read > file in matlab. Does the qdec.table.dat file need to be in certain format? > > -Sabin > > > > ___ > 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] fReadQdec question
Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin___ 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] Tutorial for linear mixed model toolbox
Hi all, I was just wondering if there is a tutorial or example on how to use linear mixed effect model toolbox for longitudinal analysis. I already processed my structural images with longitudinal processing pipeline from freesurfer. I want to do group analysis where I have 4 groups with N~20-30 on each group for time T1 and T2 scans in duration of ~2 years. I am kind of in confusion on how to proceed like making qdec.table.dat and contrast matrix and all. Thanks for help -- Cheers, Sabin ___ 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] long.qdec.table.dat question
Hi all, I am trying to use qdec to perform comparison of cortical thickness in two different time periods. So I ran recon-all base and recon-all -long. then defined long.qdec.table.dat as fsid fsid-base years MRI_001_T1 MRI_001 0 MRI_001_T2 MRI_001 2 When I tried to run qdec it says it "cant find MRI_001_T1/surf/lh.thichkeness.fwhm10.fsaverage.mgh" which I think makes sense because I did not run qcache to smooth the surface. So my question is Is the way I am writing my lon.qdec.table.dat correct or should it be fsidfsid-base years MRI_001_T1.long.MRI_001 MRI_001 0 MRI_001_T2 .long.MRI_001 MRI_001 2 Also, if I need to run qcache should I run in MRI_001_T1 or MRI_001_T1.long.MRI_001. Thanks. Sabin ___ 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 subcortical volumes
Hi all, Just to be sure, if I want to compare ICV or hippocampus volume between two time points I extract the values from aseg.stats of MRI_001.long.template and MRI_002.long.template right. Also, if thats the case is it okay if I rerun autorecon with -hippo-subfields flags for those MRI_001.long.template and MRI_002.long.template. Thanks, Sabin ___ 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 processing for lgi comparison
Hi all, Is there a longitudinal processing stream to compare local gyrification index (lgi) across two time points. -Sabin ___ 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 processing (base-tps error)
HI all, I ran longitudinal processing with reco-all -base -tp -tp -all but in base-tps file of template ID I found the subject ID of MRI_T1 twice instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able to do for MRI_T1 but could not do the same for MRI_T2. ANy help would be appreciated. Thanks SK ___ 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] -mprage flags
Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK ___ 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] control point guidance
Hi Michael, I had the same problem too. It might be because of the type of scanner you are using. I added -washu_mprage flag, it pretty much helped me (I did not had to add a lot of controls points and so on so forth. You can go through the link below. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011695.html Hope it helps. -SK On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms wrote: > > Hi guys, > > We are currently trying to fix some errors in the white/pial surfaces > where there are thin white matter strands by using control points, and > are noticing a couple things: > > 1) The resulting WM surface in the area of the CPs can end up too far > into the GM instead. Given that, is there any practical guidance for > how to think about the surrounding spatial extent that is impacted by a > given CP? i.e., How do CP's actually get used within mri_normalize in > an algorithmic sense? > > 2) The surfaces are being impacted in places distant from the CPs. > e.g., CP's placed in the left anterior temporal lobe are resulting in > surface changes in the right anterior temporal lobe. And when I > difference the original norm.mgz vs. the one obtained after using CP's, > I'm seeing an odd pattern of intensity differences which is clearly not > limited to just the area of the CP's (which would be my expectation). > > This is version 5.1. > > thanks, > -MH > > > -- > Michael Harms, Ph.D. > > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > Renard Hospital, Room 6604 Tel: 314-747-6173 > 660 South Euclid Ave.Fax: 314-747-2182 > St. Louis, MO 63110 Email: mha...@wustl.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] wm edit freeview
Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK ___ 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.
